PDB Short entry for 3GCX HEADER PROTEIN BINDING 22-FEB-09 3GCX TITLE PCSK9:EGFA (PH 7.4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 3 CHAIN: P; COMPND 4 SYNONYM: PROPROTEIN CONVERTASE PC9, SUBTILISIN/KEXIN-LIKE PROTEASE COMPND 5 PC9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 10 CHAIN: A; COMPND 11 SYNONYM: PROPROTEIN CONVERTASE PC9, SUBTILISIN/KEXIN-LIKE PROTEASE COMPND 12 PC9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1; COMPND 13 EC: 3.4.21.-; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 17 CHAIN: E; COMPND 18 SYNONYM: LDL RECEPTOR; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCSK9, NARC1, PSEC0052; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HUMAN EMBRYONIC KIDNEY CELLS (HEK293S); SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: PCSK9, NARC1, PSEC0052; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HUMAN EMBRYONIC KIDNEY CELLS (HEK293S); SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: LDLR; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PCSK9, LDL RECEPTOR, AUTOCATALYTIC CLEAVAGE, CHOLESTEROL METABOLISM, KEYWDS 2 DISEASE MUTATION, GLYCOPROTEIN, HYDROLASE, LIPID METABOLISM, KEYWDS 3 PHOSPHOPROTEIN, PROTEASE, SECRETED, SERINE PROTEASE, STEROID KEYWDS 4 METABOLISM, ZYMOGEN, COATED PIT, EGF-LIKE DOMAIN, ENDOCYTOSIS, HOST- KEYWDS 5 VIRUS INTERACTION, LDL, LIPID TRANSPORT, MEMBRANE, RECEPTOR, KEYWDS 6 TRANSMEMBRANE, TRANSPORT, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.C.MCNUTT,H.J.KWON,C.CHEN,J.R.CHEN,J.D.HORTON,T.A.LAGACE REVDAT 4 06-SEP-23 3GCX 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3GCX 1 VERSN REVDAT 2 28-APR-09 3GCX 1 JRNL REVDAT 1 03-MAR-09 3GCX 0 JRNL AUTH M.C.MCNUTT,H.J.KWON,C.CHEN,J.R.CHEN,J.D.HORTON,T.A.LAGACE JRNL TITL ANTAGONISM OF SECRETED PCSK9 INCREASES LOW DENSITY JRNL TITL 2 LIPOPROTEIN RECEPTOR EXPRESSION IN HEPG2 CELLS. JRNL REF J.BIOL.CHEM. V. 284 10561 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19224862 JRNL DOI 10.1074/JBC.M808802200 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 23589 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1270 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1423 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.4650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : 1.08000 REMARK 3 B33 (A**2) : -2.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.510 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.308 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.236 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.073 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4364 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5924 ; 0.973 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 559 ; 5.110 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;32.180 ;23.081 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 704 ;16.017 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;14.191 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 676 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3293 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1736 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2914 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 119 ; 0.108 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.105 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.153 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.103 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2868 ; 0.295 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4494 ; 0.540 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1651 ; 0.635 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1430 ; 1.099 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 292 E 332 REMARK 3 RESIDUE RANGE : E 1 E 1 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1230 -34.3320 -1.3340 REMARK 3 T TENSOR REMARK 3 T11: 0.4842 T22: 0.1280 REMARK 3 T33: 0.0448 T12: -0.4463 REMARK 3 T13: -0.1250 T23: 0.1686 REMARK 3 L TENSOR REMARK 3 L11: 8.6026 L22: 8.0542 REMARK 3 L33: 9.5449 L12: 0.9213 REMARK 3 L13: 0.9912 L23: -1.5090 REMARK 3 S TENSOR REMARK 3 S11: -0.1756 S12: -0.1494 S13: -0.1640 REMARK 3 S21: 0.2961 S22: 0.0035 S23: 1.0366 REMARK 3 S31: 0.5245 S32: -1.2594 S33: 0.1721 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : P 61 P 152 REMARK 3 RESIDUE RANGE : A 153 A 449 REMARK 3 ORIGIN FOR THE GROUP (A): 30.9910 -8.2090 -0.0530 REMARK 3 T TENSOR REMARK 3 T11: -0.1611 T22: -0.1563 REMARK 3 T33: -0.1671 T12: 0.0156 REMARK 3 T13: -0.0096 T23: 0.1164 REMARK 3 L TENSOR REMARK 3 L11: 1.7409 L22: 2.3377 REMARK 3 L33: 3.5394 L12: -0.0223 REMARK 3 L13: 0.7747 L23: 0.3146 REMARK 3 S TENSOR REMARK 3 S11: -0.0722 S12: 0.0647 S13: 0.0974 REMARK 3 S21: 0.0611 S22: 0.2428 S23: -0.1010 REMARK 3 S31: 0.1881 S32: -0.0737 S33: -0.1706 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 453 A 682 REMARK 3 ORIGIN FOR THE GROUP (A): 29.0300 9.3080 -25.1240 REMARK 3 T TENSOR REMARK 3 T11: -0.1077 T22: -0.0172 REMARK 3 T33: -0.1069 T12: -0.0593 REMARK 3 T13: 0.0125 T23: 0.2203 REMARK 3 L TENSOR REMARK 3 L11: 5.0118 L22: 6.9043 REMARK 3 L33: 6.0701 L12: -0.8151 REMARK 3 L13: -1.8285 L23: 0.5399 REMARK 3 S TENSOR REMARK 3 S11: -0.0246 S12: 0.3929 S13: 0.2770 REMARK 3 S21: -0.3024 S22: 0.3351 S23: 0.3880 REMARK 3 S31: -0.3597 S32: -0.4066 S33: -0.3105 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3GCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24921 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 41.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3BPS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3M (NH4)H2PO4, PH 7.4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.81450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 58.02350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 58.02350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.40725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 58.02350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 58.02350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 100.22175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 58.02350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.02350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.40725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 58.02350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.02350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 100.22175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.81450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, A, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA P 53 REMARK 465 GLU P 54 REMARK 465 ALA P 55 REMARK 465 PRO P 56 REMARK 465 GLU P 57 REMARK 465 HIS P 58 REMARK 465 GLY P 59 REMARK 465 THR P 60 REMARK 465 PRO A 173 REMARK 465 PRO A 174 REMARK 465 ASP A 175 REMARK 465 GLY A 176 REMARK 465 ASP A 212 REMARK 465 GLY A 213 REMARK 465 THR A 214 REMARK 465 ARG A 215 REMARK 465 PHE A 216 REMARK 465 HIS A 217 REMARK 465 ARG A 218 REMARK 465 GLN A 219 REMARK 465 GLY A 450 REMARK 465 ALA A 451 REMARK 465 GLY A 452 REMARK 465 ALA A 532 REMARK 465 ASN A 533 REMARK 465 CYS A 534 REMARK 465 SER A 535 REMARK 465 VAL A 536 REMARK 465 HIS A 537 REMARK 465 THR A 538 REMARK 465 ALA A 539 REMARK 465 PRO A 540 REMARK 465 PRO A 541 REMARK 465 ALA A 542 REMARK 465 GLU A 543 REMARK 465 ALA A 544 REMARK 465 SER A 545 REMARK 465 MET A 546 REMARK 465 GLY A 547 REMARK 465 THR A 548 REMARK 465 ARG A 549 REMARK 465 VAL A 550 REMARK 465 HIS A 551 REMARK 465 CYS A 552 REMARK 465 HIS A 553 REMARK 465 GLN A 554 REMARK 465 GLN A 555 REMARK 465 GLY A 556 REMARK 465 HIS A 557 REMARK 465 VAL A 558 REMARK 465 LEU A 559 REMARK 465 THR A 560 REMARK 465 GLY A 561 REMARK 465 CYS A 562 REMARK 465 SER A 563 REMARK 465 SER A 564 REMARK 465 HIS A 565 REMARK 465 TRP A 566 REMARK 465 GLU A 567 REMARK 465 VAL A 568 REMARK 465 GLU A 569 REMARK 465 ASP A 570 REMARK 465 LEU A 571 REMARK 465 GLY A 572 REMARK 465 THR A 573 REMARK 465 HIS A 574 REMARK 465 LYS A 575 REMARK 465 PRO A 576 REMARK 465 PRO A 577 REMARK 465 VAL A 578 REMARK 465 LEU A 579 REMARK 465 ARG A 580 REMARK 465 PRO A 581 REMARK 465 ARG A 582 REMARK 465 GLY A 583 REMARK 465 GLN A 584 REMARK 465 PRO A 585 REMARK 465 ASN A 586 REMARK 465 GLN A 587 REMARK 465 CYS A 588 REMARK 465 VAL A 589 REMARK 465 GLY A 590 REMARK 465 HIS A 591 REMARK 465 ARG A 592 REMARK 465 GLU A 593 REMARK 465 ALA A 594 REMARK 465 SER A 595 REMARK 465 ILE A 596 REMARK 465 HIS A 597 REMARK 465 ALA A 598 REMARK 465 SER A 599 REMARK 465 CYS A 600 REMARK 465 CYS A 601 REMARK 465 ASP A 660 REMARK 465 VAL A 661 REMARK 465 SER A 662 REMARK 465 THR A 663 REMARK 465 THR A 664 REMARK 465 GLY A 665 REMARK 465 SER A 666 REMARK 465 THR A 667 REMARK 465 SER A 668 REMARK 465 GLU A 669 REMARK 465 GLU A 670 REMARK 465 HIS A 683 REMARK 465 LEU A 684 REMARK 465 ALA A 685 REMARK 465 GLN A 686 REMARK 465 ALA A 687 REMARK 465 SER A 688 REMARK 465 GLN A 689 REMARK 465 GLU A 690 REMARK 465 LEU A 691 REMARK 465 GLN A 692 REMARK 465 GLY E 290 REMARK 465 ALA E 291 REMARK 465 ASP E 333 REMARK 465 ILE E 334 REMARK 465 ASP E 335 REMARK 465 GLU E 336 REMARK 465 CYS E 337 REMARK 465 GLN E 338 REMARK 465 ASP E 339 REMARK 465 PRO E 340 REMARK 465 ASP E 341 REMARK 465 THR E 342 REMARK 465 CYS E 343 REMARK 465 SER E 344 REMARK 465 GLN E 345 REMARK 465 LEU E 346 REMARK 465 CYS E 347 REMARK 465 VAL E 348 REMARK 465 ASN E 349 REMARK 465 LEU E 350 REMARK 465 GLU E 351 REMARK 465 GLY E 352 REMARK 465 GLY E 353 REMARK 465 TYR E 354 REMARK 465 LYS E 355 REMARK 465 CYS E 356 REMARK 465 GLN E 357 REMARK 465 CYS E 358 REMARK 465 GLU E 359 REMARK 465 GLU E 360 REMARK 465 GLY E 361 REMARK 465 PHE E 362 REMARK 465 GLN E 363 REMARK 465 LEU E 364 REMARK 465 ASP E 365 REMARK 465 PRO E 366 REMARK 465 HIS E 367 REMARK 465 THR E 368 REMARK 465 LYS E 369 REMARK 465 ALA E 370 REMARK 465 CYS E 371 REMARK 465 LYS E 372 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS P 139 -7.93 73.10 REMARK 500 PRO A 164 -73.32 -50.82 REMARK 500 ASP A 186 -139.61 -151.11 REMARK 500 GLU A 206 -6.83 -52.87 REMARK 500 PRO A 209 160.72 -36.52 REMARK 500 ASN A 254 -168.46 -79.12 REMARK 500 PRO A 288 48.45 -87.88 REMARK 500 LEU A 351 -144.61 -119.59 REMARK 500 LYS A 494 99.12 -64.75 REMARK 500 PRO A 530 -53.10 -24.26 REMARK 500 PRO A 616 -92.54 -57.93 REMARK 500 GLN A 619 -155.70 -126.04 REMARK 500 PRO A 639 -70.36 -43.24 REMARK 500 ASP A 651 -114.22 52.79 REMARK 500 HIS E 306 -91.33 -125.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR E 294 O REMARK 620 2 GLU E 296 OE1 66.1 REMARK 620 3 ASP E 310 OD1 81.7 72.3 REMARK 620 4 LEU E 311 O 161.8 124.5 87.8 REMARK 620 5 GLY E 314 O 126.2 60.9 90.6 68.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GCW RELATED DB: PDB DBREF 3GCX P 53 152 UNP Q8NBP7 PCSK9_HUMAN 53 152 DBREF 3GCX A 153 692 UNP Q8NBP7 PCSK9_HUMAN 153 692 DBREF 3GCX E 293 372 UNP P01130 LDLR_HUMAN 314 393 SEQADV 3GCX GLY E 290 UNP P01130 EXPRESSION TAG SEQADV 3GCX ALA E 291 UNP P01130 EXPRESSION TAG SEQADV 3GCX MET E 292 UNP P01130 EXPRESSION TAG SEQRES 1 P 100 ALA GLU ALA PRO GLU HIS GLY THR THR ALA THR PHE HIS SEQRES 2 P 100 ARG CYS ALA LYS ASP PRO TRP ARG LEU PRO GLY THR TYR SEQRES 3 P 100 VAL VAL VAL LEU LYS GLU GLU THR HIS LEU SER GLN SER SEQRES 4 P 100 GLU ARG THR ALA ARG ARG LEU GLN ALA GLN ALA ALA ARG SEQRES 5 P 100 ARG GLY TYR LEU THR LYS ILE LEU HIS VAL PHE HIS GLY SEQRES 6 P 100 LEU LEU PRO GLY PHE LEU VAL LYS MET SER GLY ASP LEU SEQRES 7 P 100 LEU GLU LEU ALA LEU LYS LEU PRO HIS VAL ASP TYR ILE SEQRES 8 P 100 GLU GLU ASP SER SER VAL PHE ALA GLN SEQRES 1 A 540 SER ILE PRO TRP ASN LEU GLU ARG ILE THR PRO PRO ARG SEQRES 2 A 540 TYR ARG ALA ASP GLU TYR GLN PRO PRO ASP GLY GLY SER SEQRES 3 A 540 LEU VAL GLU VAL TYR LEU LEU ASP THR SER ILE GLN SER SEQRES 4 A 540 ASP HIS ARG GLU ILE GLU GLY ARG VAL MET VAL THR ASP SEQRES 5 A 540 PHE GLU ASN VAL PRO GLU GLU ASP GLY THR ARG PHE HIS SEQRES 6 A 540 ARG GLN ALA SER LYS CYS ASP SER HIS GLY THR HIS LEU SEQRES 7 A 540 ALA GLY VAL VAL SER GLY ARG ASP ALA GLY VAL ALA LYS SEQRES 8 A 540 GLY ALA SER MET ARG SER LEU ARG VAL LEU ASN CYS GLN SEQRES 9 A 540 GLY LYS GLY THR VAL SER GLY THR LEU ILE GLY LEU GLU SEQRES 10 A 540 PHE ILE ARG LYS SER GLN LEU VAL GLN PRO VAL GLY PRO SEQRES 11 A 540 LEU VAL VAL LEU LEU PRO LEU ALA GLY GLY TYR SER ARG SEQRES 12 A 540 VAL LEU ASN ALA ALA CYS GLN ARG LEU ALA ARG ALA GLY SEQRES 13 A 540 VAL VAL LEU VAL THR ALA ALA GLY ASN PHE ARG ASP ASP SEQRES 14 A 540 ALA CYS LEU TYR SER PRO ALA SER ALA PRO GLU VAL ILE SEQRES 15 A 540 THR VAL GLY ALA THR ASN ALA GLN ASP GLN PRO VAL THR SEQRES 16 A 540 LEU GLY THR LEU GLY THR ASN PHE GLY ARG CYS VAL ASP SEQRES 17 A 540 LEU PHE ALA PRO GLY GLU ASP ILE ILE GLY ALA SER SER SEQRES 18 A 540 ASP CYS SER THR CYS PHE VAL SER GLN SER GLY THR SER SEQRES 19 A 540 GLN ALA ALA ALA HIS VAL ALA GLY ILE ALA ALA MET MET SEQRES 20 A 540 LEU SER ALA GLU PRO GLU LEU THR LEU ALA GLU LEU ARG SEQRES 21 A 540 GLN ARG LEU ILE HIS PHE SER ALA LYS ASP VAL ILE ASN SEQRES 22 A 540 GLU ALA TRP PHE PRO GLU ASP GLN ARG VAL LEU THR PRO SEQRES 23 A 540 ASN LEU VAL ALA ALA LEU PRO PRO SER THR HIS GLY ALA SEQRES 24 A 540 GLY TRP GLN LEU PHE CYS ARG THR VAL TRP SER ALA HIS SEQRES 25 A 540 SER GLY PRO THR ARG MET ALA THR ALA ILE ALA ARG CYS SEQRES 26 A 540 ALA PRO ASP GLU GLU LEU LEU SER CYS SER SER PHE SER SEQRES 27 A 540 ARG SER GLY LYS ARG ARG GLY GLU ARG MET GLU ALA GLN SEQRES 28 A 540 GLY GLY LYS LEU VAL CYS ARG ALA HIS ASN ALA PHE GLY SEQRES 29 A 540 GLY GLU GLY VAL TYR ALA ILE ALA ARG CYS CYS LEU LEU SEQRES 30 A 540 PRO GLN ALA ASN CYS SER VAL HIS THR ALA PRO PRO ALA SEQRES 31 A 540 GLU ALA SER MET GLY THR ARG VAL HIS CYS HIS GLN GLN SEQRES 32 A 540 GLY HIS VAL LEU THR GLY CYS SER SER HIS TRP GLU VAL SEQRES 33 A 540 GLU ASP LEU GLY THR HIS LYS PRO PRO VAL LEU ARG PRO SEQRES 34 A 540 ARG GLY GLN PRO ASN GLN CYS VAL GLY HIS ARG GLU ALA SEQRES 35 A 540 SER ILE HIS ALA SER CYS CYS HIS ALA PRO GLY LEU GLU SEQRES 36 A 540 CYS LYS VAL LYS GLU HIS GLY ILE PRO ALA PRO GLN GLU SEQRES 37 A 540 GLN VAL THR VAL ALA CYS GLU GLU GLY TRP THR LEU THR SEQRES 38 A 540 GLY CYS SER ALA LEU PRO GLY THR SER HIS VAL LEU GLY SEQRES 39 A 540 ALA TYR ALA VAL ASP ASN THR CYS VAL VAL ARG SER ARG SEQRES 40 A 540 ASP VAL SER THR THR GLY SER THR SER GLU GLU ALA VAL SEQRES 41 A 540 THR ALA VAL ALA ILE CYS CYS ARG SER ARG HIS LEU ALA SEQRES 42 A 540 GLN ALA SER GLN GLU LEU GLN SEQRES 1 E 83 GLY ALA MET GLY THR ASN GLU CYS LEU ASP ASN ASN GLY SEQRES 2 E 83 GLY CYS SER HIS VAL CYS ASN ASP LEU LYS ILE GLY TYR SEQRES 3 E 83 GLU CYS LEU CYS PRO ASP GLY PHE GLN LEU VAL ALA GLN SEQRES 4 E 83 ARG ARG CYS GLU ASP ILE ASP GLU CYS GLN ASP PRO ASP SEQRES 5 E 83 THR CYS SER GLN LEU CYS VAL ASN LEU GLU GLY GLY TYR SEQRES 6 E 83 LYS CYS GLN CYS GLU GLU GLY PHE GLN LEU ASP PRO HIS SEQRES 7 E 83 THR LYS ALA CYS LYS HET CA E 1 1 HETNAM CA CALCIUM ION FORMUL 4 CA CA 2+ HELIX 1 1 LYS P 69 PRO P 71 5 3 HELIX 2 2 HIS P 87 ARG P 105 1 19 HELIX 3 3 SER P 127 ASP P 129 5 3 HELIX 4 4 LEU P 130 LYS P 136 1 7 HELIX 5 5 PRO A 155 ILE A 161 1 7 HELIX 6 6 ARG A 167 TYR A 171 5 5 HELIX 7 7 ASP A 224 GLY A 236 1 13 HELIX 8 8 VAL A 261 GLN A 278 1 18 HELIX 9 9 SER A 294 ALA A 307 1 14 HELIX 10 10 ASP A 321 CYS A 323 5 3 HELIX 11 11 GLY A 384 GLU A 403 1 20 HELIX 12 12 THR A 407 PHE A 418 1 12 HELIX 13 13 ASN A 425 PHE A 429 5 5 HELIX 14 14 PRO A 430 VAL A 435 1 6 HELIX 15 15 ASN E 295 CYS E 304 5 10 SHEET 1 A 3 THR P 63 HIS P 65 0 SHEET 2 A 3 VAL P 140 ALA P 151 1 O GLU P 145 N HIS P 65 SHEET 3 A 3 LYS A 258 THR A 260 -1 O GLY A 259 N VAL P 149 SHEET 1 B 6 LYS P 110 PHE P 115 0 SHEET 2 B 6 GLY P 121 LYS P 125 -1 O LYS P 125 N LYS P 110 SHEET 3 B 6 ARG P 73 LEU P 82 -1 N VAL P 80 O PHE P 122 SHEET 4 B 6 VAL P 140 ALA P 151 -1 O ASP P 146 N THR P 77 SHEET 5 B 6 LEU A 289 GLY A 292 -1 O ALA A 290 N PHE P 150 SHEET 6 B 6 TYR A 325 SER A 326 -1 O SER A 326 N GLY A 291 SHEET 1 C 7 VAL A 200 THR A 203 0 SHEET 2 C 7 SER A 246 ARG A 251 1 O SER A 249 N MET A 201 SHEET 3 C 7 GLU A 181 ASP A 186 1 N LEU A 184 O LEU A 250 SHEET 4 C 7 LEU A 283 LEU A 287 1 O LEU A 286 N TYR A 183 SHEET 5 C 7 VAL A 310 ALA A 314 1 O VAL A 310 N VAL A 285 SHEET 6 C 7 ILE A 334 THR A 339 1 O ILE A 334 N LEU A 311 SHEET 7 C 7 LEU A 361 PRO A 364 1 O LEU A 361 N GLY A 337 SHEET 1 D 2 THR A 347 LEU A 348 0 SHEET 2 D 2 LEU A 351 GLY A 352 -1 O LEU A 351 N LEU A 348 SHEET 1 E 4 ILE A 368 ALA A 371 0 SHEET 2 E 4 CYS A 378 GLN A 382 -1 O VAL A 380 N GLY A 370 SHEET 3 E 4 VAL E 307 ASN E 309 -1 O CYS E 308 N PHE A 379 SHEET 4 E 4 GLU E 316 LEU E 318 -1 O LEU E 318 N VAL E 307 SHEET 1 F 2 ALA A 420 LYS A 421 0 SHEET 2 F 2 LEU A 440 VAL A 441 -1 O VAL A 441 N ALA A 420 SHEET 1 G 3 PHE A 456 TRP A 461 0 SHEET 2 G 3 TYR A 521 LEU A 528 -1 O ALA A 524 N VAL A 460 SHEET 3 G 3 GLU A 482 PHE A 489 -1 N SER A 487 O ILE A 523 SHEET 1 H 3 THR A 472 ALA A 475 0 SHEET 2 H 3 LYS A 506 ASN A 513 -1 O CYS A 509 N ALA A 475 SHEET 3 H 3 ARG A 495 GLN A 503 -1 N GLU A 501 O VAL A 508 SHEET 1 I 3 LEU A 606 ILE A 615 0 SHEET 2 I 3 VAL A 672 SER A 681 -1 O ALA A 676 N LYS A 611 SHEET 3 I 3 THR A 631 LEU A 638 -1 N THR A 631 O CYS A 679 SHEET 1 J 3 GLN A 621 ALA A 625 0 SHEET 2 J 3 THR A 653 SER A 658 -1 O CYS A 654 N VAL A 624 SHEET 3 J 3 VAL A 644 VAL A 650 -1 N TYR A 648 O VAL A 655 SHEET 1 K 2 GLN E 324 VAL E 326 0 SHEET 2 K 2 ARG E 330 GLU E 332 -1 O ARG E 330 N VAL E 326 SSBOND 1 CYS A 223 CYS A 255 1555 1555 2.04 SSBOND 2 CYS A 323 CYS A 358 1555 1555 2.06 SSBOND 3 CYS A 375 CYS A 378 1555 1555 2.05 SSBOND 4 CYS A 457 CYS A 527 1555 1555 2.05 SSBOND 5 CYS A 477 CYS A 526 1555 1555 2.04 SSBOND 6 CYS A 486 CYS A 509 1555 1555 2.06 SSBOND 7 CYS A 608 CYS A 679 1555 1555 2.05 SSBOND 8 CYS A 626 CYS A 678 1555 1555 2.05 SSBOND 9 CYS A 635 CYS A 654 1555 1555 2.04 SSBOND 10 CYS E 297 CYS E 308 1555 1555 2.04 SSBOND 11 CYS E 304 CYS E 317 1555 1555 2.04 SSBOND 12 CYS E 319 CYS E 331 1555 1555 2.04 LINK CA CA E 1 O THR E 294 1555 1555 2.58 LINK CA CA E 1 OE1 GLU E 296 1555 1555 2.82 LINK CA CA E 1 OD1 ASP E 310 1555 1555 2.27 LINK CA CA E 1 O LEU E 311 1555 1555 2.39 LINK CA CA E 1 O GLY E 314 1555 1555 2.94 CISPEP 1 SER A 326 PRO A 327 0 2.32 SITE 1 AC1 6 MET E 292 THR E 294 GLU E 296 ASP E 310 SITE 2 AC1 6 LEU E 311 GLY E 314 CRYST1 116.047 116.047 133.629 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007483 0.00000