PDB Short entry for 3RIE HEADER TRANSFERASE/TRANSFERASE INHIBITOR 13-APR-11 3RIE TITLE THE STRUCTURE OF PLASMODIUM FALCIPARUM SPERMIDINE SYNTHASE IN COMPLEX TITLE 2 WITH 5'-METHYLTHIOADENOSINE AND N-(3-AMINOPROPYL)-TRANS-CYCLOHEXANE- TITLE 3 1,4-DIAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMIDINE SYNTHASE; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 41-321; COMPND 5 EC: 2.5.1.16; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: PF11_0301; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15-TEV-LIC KEYWDS ROSSMANN-LIKE FOLD, ROSSMANN FOLD, SPERMIDINE SYNTHESIS, AMINOPROPYL KEYWDS 2 TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.WILLIAMS,J.SPRENGER,L.PERSSON,A.I.LOUW,L.BIRKHOLTZ,S.AL-KARADAGHI REVDAT 6 13-SEP-23 3RIE 1 REMARK SEQADV REVDAT 5 04-SEP-19 3RIE 1 REMARK REVDAT 4 17-JUL-19 3RIE 1 REMARK REVDAT 3 07-MAR-18 3RIE 1 REMARK REVDAT 2 25-FEB-15 3RIE 1 JRNL REVDAT 1 25-APR-12 3RIE 0 JRNL AUTH P.B.BURGER,M.WILLIAMS,J.SPRENGER,S.B.REEKSTING,M.BOTHA, JRNL AUTH 2 I.B.MULLER,F.JOUBERT,L.M.BIRKHOLTZ,A.I.LOUW JRNL TITL A NOVEL INHIBITOR OF PLASMODIUM FALCIPARUM SPERMIDINE JRNL TITL 2 SYNTHASE: A TWIST IN THE TAIL. JRNL REF MALAR J V. 14 54 2015 JRNL REFN ESSN 1475-2875 JRNL PMID 25651815 JRNL DOI 10.1186/S12936-015-0572-Z REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 93239 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5053 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 260 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6745 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 131 REMARK 3 SOLVENT ATOMS : 617 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.65000 REMARK 3 B22 (A**2) : -1.70000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.67000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.923 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.029 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 2.100 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; 6.768 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4 REMARK 4 3RIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04 REMARK 200 MONOCHROMATOR : BENT SI (111) CRYSTAL REMARK 200 OPTICS : MULTILAYER MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2HTE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M AMMONIUM SULFATE, REMARK 280 0.1M 2-(N-MORPHOLINO) ETHANESULFONIC ACID, PH 5.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 98.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 67.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 98.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 67.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -3.84429 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.30728 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 839 LIES ON A SPECIAL POSITION. 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 GLY A 39 REMARK 465 SER A 40 REMARK 465 GLY B 39 REMARK 465 SER B 40 REMARK 465 ASN B 320 REMARK 465 ILE B 321 REMARK 465 GLY C 39 REMARK 465 SER C 40 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 41 NZ REMARK 480 LYS A 62 NZ REMARK 480 LYS A 68 CE NZ REMARK 480 ASP A 278 CG OD1 OD2 REMARK 480 LYS A 297 NZ REMARK 480 LYS B 70 CD CE NZ REMARK 480 LYS B 252 CE NZ REMARK 480 LYS C 283 NZ 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 ASP A 196 69.74 -105.29 REMARK 500 SER A 198 -178.64 -64.90 REMARK 500 ILE A 235 -75.16 -118.04 REMARK 500 TYR A 298 -44.94 -130.56 REMARK 500 ASP B 196 67.67 -109.06 REMARK 500 GLU B 231 165.32 43.78 REMARK 500 TYR B 298 -63.99 -131.34 REMARK 500 GLU C 177 147.66 -173.09 REMARK 500 ASP C 196 72.48 -101.57 REMARK 500 PHE C 208 58.13 -116.00 REMARK 500 CYS C 230 42.38 -141.17 REMARK 500 GLU C 231 -170.89 71.67 REMARK 500 ILE C 235 -10.59 -141.79 REMARK 500 TYR C 298 -62.67 -128.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE B 318 GLU B 319 144.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 971 DISTANCE = 6.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JFQ A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JFQ B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PG C 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JFQ C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 601 DBREF 3RIE A 41 321 UNP Q8II73 Q8II73_PLAF7 41 321 DBREF 3RIE B 41 321 UNP Q8II73 Q8II73_PLAF7 41 321 DBREF 3RIE C 41 321 UNP Q8II73 Q8II73_PLAF7 41 321 SEQADV 3RIE GLY A 39 UNP Q8II73 EXPRESSION TAG SEQADV 3RIE SER A 40 UNP Q8II73 EXPRESSION TAG SEQADV 3RIE GLY B 39 UNP Q8II73 EXPRESSION TAG SEQADV 3RIE SER B 40 UNP Q8II73 EXPRESSION TAG SEQADV 3RIE GLY C 39 UNP Q8II73 EXPRESSION TAG SEQADV 3RIE SER C 40 UNP Q8II73 EXPRESSION TAG SEQRES 1 A 283 GLY SER LYS LYS TRP PHE SER GLU PHE SER ILE MET TRP SEQRES 2 A 283 PRO GLY GLN ALA PHE SER LEU LYS ILE LYS LYS ILE LEU SEQRES 3 A 283 TYR GLU THR LYS SER LYS TYR GLN ASN VAL LEU VAL PHE SEQRES 4 A 283 GLU SER THR THR TYR GLY LYS VAL LEU VAL LEU ASP GLY SEQRES 5 A 283 VAL ILE GLN LEU THR GLU LYS ASP GLU PHE ALA TYR HIS SEQRES 6 A 283 GLU MET MET THR HIS VAL PRO MET THR VAL SER LYS GLU SEQRES 7 A 283 PRO LYS ASN VAL LEU VAL VAL GLY GLY GLY ASP GLY GLY SEQRES 8 A 283 ILE ILE ARG GLU LEU CYS LYS TYR LYS SER VAL GLU ASN SEQRES 9 A 283 ILE ASP ILE CYS GLU ILE ASP GLU THR VAL ILE GLU VAL SEQRES 10 A 283 SER LYS ILE TYR PHE LYS ASN ILE SER CYS GLY TYR GLU SEQRES 11 A 283 ASP LYS ARG VAL ASN VAL PHE ILE GLU ASP ALA SER LYS SEQRES 12 A 283 PHE LEU GLU ASN VAL THR ASN THR TYR ASP VAL ILE ILE SEQRES 13 A 283 VAL ASP SER SER ASP PRO ILE GLY PRO ALA GLU THR LEU SEQRES 14 A 283 PHE ASN GLN ASN PHE TYR GLU LYS ILE TYR ASN ALA LEU SEQRES 15 A 283 LYS PRO ASN GLY TYR CYS VAL ALA GLN CYS GLU SER LEU SEQRES 16 A 283 TRP ILE HIS VAL GLY THR ILE LYS ASN MET ILE GLY TYR SEQRES 17 A 283 ALA LYS LYS LEU PHE LYS LYS VAL GLU TYR ALA ASN ILE SEQRES 18 A 283 SER ILE PRO THR TYR PRO CYS GLY CYS ILE GLY ILE LEU SEQRES 19 A 283 CYS CYS SER LYS THR ASP THR GLY LEU THR LYS PRO ASN SEQRES 20 A 283 LYS LYS LEU GLU SER LYS GLU PHE ALA ASP LEU LYS TYR SEQRES 21 A 283 TYR ASN TYR GLU ASN HIS SER ALA ALA PHE LYS LEU PRO SEQRES 22 A 283 ALA PHE LEU LEU LYS GLU ILE GLU ASN ILE SEQRES 1 B 283 GLY SER LYS LYS TRP PHE SER GLU PHE SER ILE MET TRP SEQRES 2 B 283 PRO GLY GLN ALA PHE SER LEU LYS ILE LYS LYS ILE LEU SEQRES 3 B 283 TYR GLU THR LYS SER LYS TYR GLN ASN VAL LEU VAL PHE SEQRES 4 B 283 GLU SER THR THR TYR GLY LYS VAL LEU VAL LEU ASP GLY SEQRES 5 B 283 VAL ILE GLN LEU THR GLU LYS ASP GLU PHE ALA TYR HIS SEQRES 6 B 283 GLU MET MET THR HIS VAL PRO MET THR VAL SER LYS GLU SEQRES 7 B 283 PRO LYS ASN VAL LEU VAL VAL GLY GLY GLY ASP GLY GLY SEQRES 8 B 283 ILE ILE ARG GLU LEU CYS LYS TYR LYS SER VAL GLU ASN SEQRES 9 B 283 ILE ASP ILE CYS GLU ILE ASP GLU THR VAL ILE GLU VAL SEQRES 10 B 283 SER LYS ILE TYR PHE LYS ASN ILE SER CYS GLY TYR GLU SEQRES 11 B 283 ASP LYS ARG VAL ASN VAL PHE ILE GLU ASP ALA SER LYS SEQRES 12 B 283 PHE LEU GLU ASN VAL THR ASN THR TYR ASP VAL ILE ILE SEQRES 13 B 283 VAL ASP SER SER ASP PRO ILE GLY PRO ALA GLU THR LEU SEQRES 14 B 283 PHE ASN GLN ASN PHE TYR GLU LYS ILE TYR ASN ALA LEU SEQRES 15 B 283 LYS PRO ASN GLY TYR CYS VAL ALA GLN CYS GLU SER LEU SEQRES 16 B 283 TRP ILE HIS VAL GLY THR ILE LYS ASN MET ILE GLY TYR SEQRES 17 B 283 ALA LYS LYS LEU PHE LYS LYS VAL GLU TYR ALA ASN ILE SEQRES 18 B 283 SER ILE PRO THR TYR PRO CYS GLY CYS ILE GLY ILE LEU SEQRES 19 B 283 CYS CYS SER LYS THR ASP THR GLY LEU THR LYS PRO ASN SEQRES 20 B 283 LYS LYS LEU GLU SER LYS GLU PHE ALA ASP LEU LYS TYR SEQRES 21 B 283 TYR ASN TYR GLU ASN HIS SER ALA ALA PHE LYS LEU PRO SEQRES 22 B 283 ALA PHE LEU LEU LYS GLU ILE GLU ASN ILE SEQRES 1 C 283 GLY SER LYS LYS TRP PHE SER GLU PHE SER ILE MET TRP SEQRES 2 C 283 PRO GLY GLN ALA PHE SER LEU LYS ILE LYS LYS ILE LEU SEQRES 3 C 283 TYR GLU THR LYS SER LYS TYR GLN ASN VAL LEU VAL PHE SEQRES 4 C 283 GLU SER THR THR TYR GLY LYS VAL LEU VAL LEU ASP GLY SEQRES 5 C 283 VAL ILE GLN LEU THR GLU LYS ASP GLU PHE ALA TYR HIS SEQRES 6 C 283 GLU MET MET THR HIS VAL PRO MET THR VAL SER LYS GLU SEQRES 7 C 283 PRO LYS ASN VAL LEU VAL VAL GLY GLY GLY ASP GLY GLY SEQRES 8 C 283 ILE ILE ARG GLU LEU CYS LYS TYR LYS SER VAL GLU ASN SEQRES 9 C 283 ILE ASP ILE CYS GLU ILE ASP GLU THR VAL ILE GLU VAL SEQRES 10 C 283 SER LYS ILE TYR PHE LYS ASN ILE SER CYS GLY TYR GLU SEQRES 11 C 283 ASP LYS ARG VAL ASN VAL PHE ILE GLU ASP ALA SER LYS SEQRES 12 C 283 PHE LEU GLU ASN VAL THR ASN THR TYR ASP VAL ILE ILE SEQRES 13 C 283 VAL ASP SER SER ASP PRO ILE GLY PRO ALA GLU THR LEU SEQRES 14 C 283 PHE ASN GLN ASN PHE TYR GLU LYS ILE TYR ASN ALA LEU SEQRES 15 C 283 LYS PRO ASN GLY TYR CYS VAL ALA GLN CYS GLU SER LEU SEQRES 16 C 283 TRP ILE HIS VAL GLY THR ILE LYS ASN MET ILE GLY TYR SEQRES 17 C 283 ALA LYS LYS LEU PHE LYS LYS VAL GLU TYR ALA ASN ILE SEQRES 18 C 283 SER ILE PRO THR TYR PRO CYS GLY CYS ILE GLY ILE LEU SEQRES 19 C 283 CYS CYS SER LYS THR ASP THR GLY LEU THR LYS PRO ASN SEQRES 20 C 283 LYS LYS LEU GLU SER LYS GLU PHE ALA ASP LEU LYS TYR SEQRES 21 C 283 TYR ASN TYR GLU ASN HIS SER ALA ALA PHE LYS LEU PRO SEQRES 22 C 283 ALA PHE LEU LEU LYS GLU ILE GLU ASN ILE HET MTA A 401 20 HET JFQ A 501 12 HET GOL A 601 6 HET MTA B 401 20 HET JFQ B 501 12 HET GOL B 602 6 HET 1PG C 701 17 HET MTA C 401 20 HET JFQ C 501 12 HET GOL C 601 6 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETNAM JFQ TRANS-N-(3-AMINOPROPYL)CYCLOHEXANE-1,4-DIAMINE HETNAM GOL GLYCEROL HETNAM 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)- HETNAM 2 1PG ETHANOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MTA 3(C11 H15 N5 O3 S) FORMUL 5 JFQ 3(C9 H21 N3) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 10 1PG C11 H24 O6 FORMUL 14 HOH *617(H2 O) HELIX 1 1 ASP A 98 SER A 114 1 17 HELIX 2 2 GLY A 128 LYS A 136 1 9 HELIX 3 3 ASP A 149 PHE A 160 1 12 HELIX 4 4 SER A 164 ASP A 169 5 6 HELIX 5 5 ASP A 178 VAL A 186 1 9 HELIX 6 6 GLY A 202 PHE A 208 5 7 HELIX 7 7 ASN A 209 ALA A 219 1 11 HELIX 8 8 HIS A 236 LYS A 249 1 14 HELIX 9 9 TYR A 264 CYS A 266 5 3 HELIX 10 10 SER A 290 ALA A 294 5 5 HELIX 11 11 ASN A 300 ALA A 307 1 8 HELIX 12 12 PRO A 311 ILE A 318 1 8 HELIX 13 13 ASP B 98 THR B 112 1 15 HELIX 14 14 GLY B 128 LYS B 136 1 9 HELIX 15 15 ASP B 149 PHE B 160 1 12 HELIX 16 16 PHE B 160 CYS B 165 1 6 HELIX 17 17 GLY B 166 ASP B 169 5 4 HELIX 18 18 ASP B 178 LEU B 183 1 6 HELIX 19 19 GLU B 184 VAL B 186 5 3 HELIX 20 20 GLY B 202 PHE B 208 5 7 HELIX 21 21 ASN B 209 ALA B 219 1 11 HELIX 22 22 HIS B 236 LYS B 249 1 14 HELIX 23 23 TYR B 264 CYS B 266 5 3 HELIX 24 24 SER B 290 ALA B 294 5 5 HELIX 25 25 ASN B 300 ALA B 307 1 8 HELIX 26 26 PRO B 311 GLU B 319 1 9 HELIX 27 27 ASP C 98 SER C 114 1 17 HELIX 28 28 GLY C 128 CYS C 135 1 8 HELIX 29 29 ASP C 149 PHE C 160 1 12 HELIX 30 30 SER C 164 ASP C 169 5 6 HELIX 31 31 ASP C 178 LEU C 183 1 6 HELIX 32 32 GLU C 184 VAL C 186 5 3 HELIX 33 33 GLY C 202 PHE C 208 5 7 HELIX 34 34 ASN C 209 ALA C 219 1 11 HELIX 35 35 HIS C 236 LYS C 249 1 14 HELIX 36 36 TYR C 264 CYS C 266 5 3 HELIX 37 37 SER C 290 ALA C 294 5 5 HELIX 38 38 ASN C 300 ALA C 307 1 8 HELIX 39 39 PRO C 311 ASN C 320 1 10 SHEET 1 A 5 TRP A 43 GLU A 46 0 SHEET 2 A 5 PHE A 56 LYS A 68 -1 O LEU A 58 N PHE A 44 SHEET 3 A 5 ASN A 73 SER A 79 -1 O VAL A 76 N LEU A 64 SHEET 4 A 5 LYS A 84 LEU A 88 -1 O VAL A 87 N LEU A 75 SHEET 5 A 5 VAL A 91 THR A 95 -1 O GLN A 93 N LEU A 86 SHEET 1 B 7 VAL A 172 ILE A 176 0 SHEET 2 B 7 ASN A 142 GLU A 147 1 N ILE A 145 O PHE A 175 SHEET 3 B 7 ASN A 119 GLY A 124 1 N GLY A 124 O CYS A 146 SHEET 4 B 7 TYR A 190 ASP A 196 1 O ILE A 194 N VAL A 123 SHEET 5 B 7 LEU A 220 CYS A 230 1 O LYS A 221 N TYR A 190 SHEET 6 B 7 CYS A 268 SER A 275 -1 O CYS A 274 N CYS A 226 SHEET 7 B 7 LYS A 253 SER A 260 -1 N GLU A 255 O CYS A 273 SHEET 1 C 4 TRP B 43 GLU B 46 0 SHEET 2 C 4 GLN B 54 LYS B 68 -1 O LEU B 58 N PHE B 44 SHEET 3 C 4 GLN C 54 LYS C 68 -1 O SER C 57 N ALA B 55 SHEET 4 C 4 TRP C 43 GLU C 46 -1 N GLU C 46 O PHE C 56 SHEET 1 D 8 VAL B 91 THR B 95 0 SHEET 2 D 8 LYS B 84 LEU B 88 -1 N LEU B 86 O GLN B 93 SHEET 3 D 8 ASN B 73 SER B 79 -1 N PHE B 77 O VAL B 85 SHEET 4 D 8 GLN B 54 LYS B 68 -1 N LYS B 62 O GLU B 78 SHEET 5 D 8 GLN C 54 LYS C 68 -1 O SER C 57 N ALA B 55 SHEET 6 D 8 ASN C 73 SER C 79 -1 O GLU C 78 N LYS C 62 SHEET 7 D 8 LYS C 84 LEU C 88 -1 O VAL C 87 N LEU C 75 SHEET 8 D 8 VAL C 91 THR C 95 -1 O GLN C 93 N LEU C 86 SHEET 1 E 7 VAL B 172 PHE B 175 0 SHEET 2 E 7 ASN B 142 CYS B 146 1 N ILE B 145 O PHE B 175 SHEET 3 E 7 ASN B 119 GLY B 124 1 N GLY B 124 O CYS B 146 SHEET 4 E 7 TYR B 190 ASP B 196 1 O ASP B 191 N ASN B 119 SHEET 5 E 7 LEU B 220 GLN B 229 1 O VAL B 227 N VAL B 195 SHEET 6 E 7 CYS B 268 SER B 275 -1 O CYS B 274 N CYS B 226 SHEET 7 E 7 LYS B 253 SER B 260 -1 N LYS B 253 O SER B 275 SHEET 1 F 7 VAL C 172 ILE C 176 0 SHEET 2 F 7 ASN C 142 GLU C 147 1 N ILE C 145 O PHE C 175 SHEET 3 F 7 ASN C 119 GLY C 124 1 N GLY C 124 O CYS C 146 SHEET 4 F 7 TYR C 190 ASP C 196 1 O ILE C 194 N LEU C 121 SHEET 5 F 7 LEU C 220 GLN C 229 1 O VAL C 227 N VAL C 195 SHEET 6 F 7 CYS C 268 SER C 275 -1 O CYS C 274 N CYS C 226 SHEET 7 F 7 LYS C 253 SER C 260 -1 N GLU C 255 O CYS C 273 SITE 1 AC1 19 GLN A 72 LEU A 88 GLN A 93 GLY A 124 SITE 2 AC1 19 GLY A 125 ASP A 127 CYS A 146 GLU A 147 SITE 3 AC1 19 ILE A 148 ASP A 149 VAL A 152 ASP A 178 SITE 4 AC1 19 ALA A 179 ASP A 196 SER A 198 PRO A 203 SITE 5 AC1 19 ALA A 204 THR A 206 JFQ A 501 SITE 1 AC2 12 ILE A 92 GLN A 93 TYR A 102 HIS A 103 SITE 2 AC2 12 ASP A 127 ASP A 196 SER A 197 ASP A 199 SITE 3 AC2 12 TYR A 264 ILE A 269 MTA A 401 HOH A 831 SITE 1 AC3 5 LYS A 97 TRP A 234 HOH A 835 HOH A 858 SITE 2 AC3 5 HOH A 927 SITE 1 AC4 21 GLN B 72 LEU B 88 GLN B 93 GLY B 124 SITE 2 AC4 21 GLY B 125 ASP B 127 CYS B 146 GLU B 147 SITE 3 AC4 21 ILE B 148 ASP B 149 VAL B 152 ASP B 178 SITE 4 AC4 21 ALA B 179 ASP B 196 SER B 197 SER B 198 SITE 5 AC4 21 PRO B 203 ALA B 204 THR B 206 LEU B 207 SITE 6 AC4 21 JFQ B 501 SITE 1 AC5 13 ILE B 92 GLN B 93 TYR B 102 HIS B 103 SITE 2 AC5 13 ASP B 127 ASP B 196 SER B 197 ASP B 199 SITE 3 AC5 13 TYR B 264 ILE B 269 MTA B 401 HOH B 802 SITE 4 AC5 13 HOH B 981 SITE 1 AC6 6 LYS B 97 LYS B 297 HOH B 946 HOH B 989 SITE 2 AC6 6 HOH B 990 TRP C 234 SITE 1 AC7 4 TRP C 43 SER C 45 PHE C 47 HOH C 989 SITE 1 AC8 19 GLN C 72 LEU C 88 GLN C 93 GLY C 124 SITE 2 AC8 19 GLY C 125 ASP C 127 CYS C 146 GLU C 147 SITE 3 AC8 19 ILE C 148 VAL C 152 ASP C 178 ALA C 179 SITE 4 AC8 19 ASP C 196 SER C 198 PRO C 203 ALA C 204 SITE 5 AC8 19 THR C 206 LEU C 207 JFQ C 501 SITE 1 AC9 13 ILE C 92 GLN C 93 TYR C 102 HIS C 103 SITE 2 AC9 13 ASP C 127 ASP C 196 SER C 197 ASP C 199 SITE 3 AC9 13 TYR C 264 ILE C 269 MTA C 401 HOH C 805 SITE 4 AC9 13 HOH C 875 SITE 1 BC1 7 TRP B 234 LYS C 97 HOH C 832 HOH C 865 SITE 2 BC1 7 HOH C 958 HOH C1010 HOH C1015 CRYST1 196.800 134.590 48.460 90.00 94.55 90.00 C 1 2 1 12 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 0.005081 0.000000 0.000404 0.00000 SCALE2 0.000000 0.007430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020701 0.00000