PDB Short entry for 2ZJI HEADER HYDROLASE 07-MAR-08 2ZJI TITLE CRYSTAL STRUCTURE OF THE HUMAN BACE1 CATALYTIC DOMAIN IN COMPLEX WITH TITLE 2 N-[1-(2,6-DIMETHOXY-BENZYL)-PIPERIDIN-4-YL]-4-MERCAPTO-BUTYRAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BACE1 CATALYTIC DOMAIN, UNP RESIDUES 43-446; COMPND 5 SYNONYM: BETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID PRECURSOR COMPND 6 PROTEIN CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, COMPND 7 MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2; COMPND 8 EC: 3.4.23.46; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BACE1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS BACE1, SMALL-MOLECULE INHIBITOR, ASPARTYL PROTEASE, GLYCOPROTEIN, KEYWDS 2 HYDROLASE, MEMBRANE, PROTEASE, TRANSMEMBRANE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR M.RANDAL,M.B.LAM,M.J.ROMANOWSKI REVDAT 4 01-NOV-23 2ZJI 1 REMARK REVDAT 3 10-NOV-21 2ZJI 1 REMARK SEQADV REVDAT 2 13-JUL-11 2ZJI 1 VERSN REVDAT 1 20-JAN-09 2ZJI 0 JRNL AUTH W.YANG,R.V.FUCINI,B.T.FAHR,M.RANDAL,K.E.LIND,M.B.LAM,W.LU, JRNL AUTH 2 Y.LU,D.R.CARY,M.J.ROMANOWSKI JRNL TITL FRAGMENT-BASED DISCOVERY OF NOVEL BACE1 INHIBITORS USING JRNL TITL 2 TETHERING TECHNOLOGY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 22764 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) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1244 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2148 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 232 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) : 34.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : -0.14000 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): 0.305 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.230 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.071 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2993 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4063 ; 0.883 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 4.970 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;37.417 ;23.459 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 469 ;14.738 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.009 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2290 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1350 ; 0.153 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1984 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 248 ; 0.093 ; 0.200 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): 52 ; 0.123 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.082 ; 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): 1870 ; 1.181 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2957 ; 2.048 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1284 ; 0.950 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1106 ; 1.542 ; 5.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 681 REMARK 3 ORIGIN FOR THE GROUP (A): 74.1225 32.3756 28.2377 REMARK 3 T TENSOR REMARK 3 T11: 0.0551 T22: 0.0479 REMARK 3 T33: 0.0535 T12: 0.0065 REMARK 3 T13: 0.0069 T23: 0.0506 REMARK 3 L TENSOR REMARK 3 L11: 2.7312 L22: 1.4121 REMARK 3 L33: 1.3814 L12: 1.9106 REMARK 3 L13: -1.2231 L23: -0.9097 REMARK 3 S TENSOR REMARK 3 S11: -0.0408 S12: 0.1135 S13: 0.3478 REMARK 3 S21: -0.0607 S22: 0.1178 S23: 0.2335 REMARK 3 S31: 0.0294 S32: -0.0978 S33: -0.0770 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: NULL REMARK 4 REMARK 4 2ZJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000028050. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24184 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07800 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35700 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2P8H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.00467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.00933 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 84.00700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 140.01167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.00233 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.00467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 112.00933 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 140.01167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 84.00700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 28.00233 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A 429 REMARK 465 LEU A 430 REMARK 465 PRO A 431 REMARK 465 ARG A 432 REMARK 465 GLU A 433 REMARK 465 THR A 434 REMARK 465 ASP A 435 REMARK 465 GLU A 436 REMARK 465 GLU A 437 REMARK 465 PRO A 438 REMARK 465 GLU A 439 REMARK 465 GLU A 440 REMARK 465 PRO A 441 REMARK 465 GLY A 442 REMARK 465 ARG A 443 REMARK 465 ALA A 157 REMARK 465 GLY A 158 REMARK 465 PHE A 159 REMARK 465 PRO A 160 REMARK 465 LEU A 161 REMARK 465 ASN A 162 REMARK 465 GLN A 163 REMARK 465 SER A 164 REMARK 465 GLU A 165 REMARK 465 VAL A 166 REMARK 465 LEU A 167 REMARK 465 ALA A 168 REMARK 465 GLU A 310 REMARK 465 ASP A 311 REMARK 465 VAL A 312 REMARK 465 ALA A 313 REMARK 465 THR A 314 REMARK 465 SER A 315 REMARK 465 GLN A 316 REMARK 465 ASP A 317 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 73 CG CD OE1 NE2 REMARK 470 LYS A 256 CB CG CD CE NZ REMARK 470 GLN A 266 CG CD OE1 NE2 REMARK 470 TRP A 270 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 REMARK 470 TRP A 270 CH2 REMARK 470 GLN A 271 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 329 S8 F1I A 449 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 446 -78.23 -112.33 REMARK 500 HIS A 89 40.14 -97.34 REMARK 500 TRP A 197 -79.53 -137.70 REMARK 500 ASP A 223 -74.27 81.33 REMARK 500 SER A 252 61.10 -116.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F1I A 449 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZJH RELATED DB: PDB REMARK 900 RELATED ID: 2ZJJ RELATED DB: PDB REMARK 900 RELATED ID: 2ZJK RELATED DB: PDB REMARK 900 RELATED ID: 2ZJL RELATED DB: PDB REMARK 900 RELATED ID: 2ZJM RELATED DB: PDB REMARK 900 RELATED ID: 2ZJN RELATED DB: PDB DBREF 2ZJI A 430 385 UNP P56817 BACE1_HUMAN 43 446 SEQADV 2ZJI MET A 429 UNP P56817 EXPRESSION TAG SEQADV 2ZJI CYS A 329 UNP P56817 THR 390 ENGINEERED MUTATION SEQRES 1 A 405 MET LEU PRO ARG GLU THR ASP GLU GLU PRO GLU GLU PRO SEQRES 2 A 405 GLY ARG ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU SEQRES 3 A 405 ARG GLY LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR SEQRES 4 A 405 VAL GLY SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP SEQRES 5 A 405 THR GLY SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS SEQRES 6 A 405 PRO PHE LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER SEQRES 7 A 405 THR TYR ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR SEQRES 8 A 405 THR GLN GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU SEQRES 9 A 405 VAL SER ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA SEQRES 10 A 405 ASN ILE ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE SEQRES 11 A 405 ASN GLY SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR SEQRES 12 A 405 ALA GLU ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE SEQRES 13 A 405 PHE ASP SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU SEQRES 14 A 405 PHE SER LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN SEQRES 15 A 405 GLN SER GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE SEQRES 16 A 405 ILE GLY GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU SEQRES 17 A 405 TRP TYR THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL SEQRES 18 A 405 ILE ILE VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS SEQRES 19 A 405 MET ASP CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL SEQRES 20 A 405 ASP SER GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL SEQRES 21 A 405 PHE GLU ALA ALA VAL LYS SER ILE LYS ALA ALA SER SER SEQRES 22 A 405 THR GLU LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN SEQRES 23 A 405 LEU VAL CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE SEQRES 24 A 405 PHE PRO VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR SEQRES 25 A 405 ASN GLN SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR SEQRES 26 A 405 LEU ARG PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP SEQRES 27 A 405 CYS TYR LYS PHE ALA ILE SER GLN SER SER CYS GLY THR SEQRES 28 A 405 VAL MET GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL SEQRES 29 A 405 PHE ASP ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER SEQRES 30 A 405 ALA CYS HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL SEQRES 31 A 405 GLU GLY PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY SEQRES 32 A 405 TYR ASN HET F1I A 449 24 HETNAM F1I N-[1-(2,6-DIMETHOXYBENZYL)PIPERIDIN-4-YL]-4- HETNAM 2 F1I SULFANYLBUTANAMIDE HETSYN F1I N-[1-(2,6-DIMETHOXY-BENZYL)-PIPERIDIN-4-YL]-4-MERCAPTO- HETSYN 2 F1I BUTYRAMIDE FORMUL 2 F1I C18 H28 N2 O3 S FORMUL 3 HOH *232(H2 O) HELIX 1 1 PHE A 447 VAL A 3 5 5 HELIX 2 2 GLN A 53 SER A 57 5 5 HELIX 3 3 TYR A 123 ALA A 127 5 5 HELIX 4 4 PRO A 135 THR A 144 1 10 HELIX 5 5 ASP A 180 SER A 182 5 3 HELIX 6 6 LYS A 218 TYR A 222 5 5 HELIX 7 7 LYS A 238 SER A 252 1 15 HELIX 8 8 LEU A 301 TYR A 305 1 5 HELIX 9 9 GLY A 334 GLU A 339 1 6 HELIX 10 10 ARG A 347 ARG A 349 5 3 HELIX 11 11 ASP A 378 GLY A 383 5 6 SHEET 1 A 9 ARG A 61 PRO A 70 0 SHEET 2 A 9 LYS A 75 SER A 86 -1 O LEU A 80 N LYS A 65 SHEET 3 A 9 TYR A 14 VAL A 20 -1 N THR A 19 O SER A 86 SHEET 4 A 9 LEU A 6 GLY A 8 -1 N ARG A 7 O TYR A 15 SHEET 5 A 9 VAL A 170 ILE A 176 -1 O VAL A 170 N GLY A 8 SHEET 6 A 9 PHE A 150 CYS A 155 -1 N GLN A 153 O SER A 173 SHEET 7 A 9 PHE A 341 ASP A 346 -1 O PHE A 345 N PHE A 150 SHEET 8 A 9 ARG A 351 SER A 357 -1 O ALA A 355 N TYR A 342 SHEET 9 A 9 TYR A 184 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 B13 ARG A 61 PRO A 70 0 SHEET 2 B13 LYS A 75 SER A 86 -1 O LEU A 80 N LYS A 65 SHEET 3 B13 THR A 94 ASP A 106 -1 O GLU A 104 N GLU A 77 SHEET 4 B13 PHE A 38 GLY A 41 1 N VAL A 40 O ILE A 102 SHEET 5 B13 GLY A 117 GLY A 120 -1 O ILE A 118 N ALA A 39 SHEET 6 B13 GLN A 25 ASP A 32 1 N LEU A 30 O LEU A 119 SHEET 7 B13 TYR A 14 VAL A 20 -1 N TYR A 14 O VAL A 31 SHEET 8 B13 LEU A 6 GLY A 8 -1 N ARG A 7 O TYR A 15 SHEET 9 B13 VAL A 170 ILE A 176 -1 O VAL A 170 N GLY A 8 SHEET 10 B13 PHE A 150 CYS A 155 -1 N GLN A 153 O SER A 173 SHEET 11 B13 PHE A 341 ASP A 346 -1 O PHE A 345 N PHE A 150 SHEET 12 B13 ARG A 351 SER A 357 -1 O ALA A 355 N TYR A 342 SHEET 13 B13 TYR A 184 PRO A 192 -1 N THR A 191 O ILE A 352 SHEET 1 C 4 ILE A 203 ILE A 208 0 SHEET 2 C 4 ILE A 283 MET A 288 -1 O TYR A 286 N ARG A 205 SHEET 3 C 4 GLN A 294 ILE A 300 -1 O ILE A 298 N LEU A 285 SHEET 4 C 4 ALA A 369 VAL A 375 -1 O ALA A 369 N THR A 299 SHEET 1 D 4 SER A 225 VAL A 227 0 SHEET 2 D 4 THR A 331 MET A 333 1 O MET A 333 N ILE A 226 SHEET 3 D 4 LEU A 234 PRO A 237 -1 N ARG A 235 O VAL A 332 SHEET 4 D 4 ILE A 324 SER A 327 1 O SER A 325 N LEU A 236 SHEET 1 E 3 VAL A 268 CYS A 269 0 SHEET 2 E 3 CYS A 319 PHE A 322 -1 O TYR A 320 N VAL A 268 SHEET 3 E 3 LEU A 306 PRO A 308 -1 N ARG A 307 O LYS A 321 SSBOND 1 CYS A 155 CYS A 359 1555 1555 2.04 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.03 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.03 CISPEP 1 SER A 22 PRO A 23 0 -0.60 CISPEP 2 ARG A 128 PRO A 129 0 4.75 CISPEP 3 GLY A 372 PRO A 373 0 -2.53 SITE 1 AC1 11 LEU A 30 ASP A 32 GLY A 34 TYR A 71 SITE 2 AC1 11 TRP A 76 PHE A 108 ILE A 118 ASP A 228 SITE 3 AC1 11 GLY A 230 ARG A 235 CYS A 329 CRYST1 103.306 103.306 168.014 90.00 90.00 120.00 P 61 2 2 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 0.009680 0.005589 0.000000 0.00000 SCALE2 0.000000 0.011178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005952 0.00000