PDB Short entry for 3UDN HEADER HYDROLASE/HYDROLASE INHIBITOR 28-OCT-11 3UDN TITLE CRYSTAL STRUCTURE OF BACE WITH COMPOUND 9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-SECRETASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 58-453; COMPND 5 SYNONYM: BACE, ASPARTYL PROTEASE 2, ASP2, ASP 2, BETA-SITE AMYLOID COMPND 6 PRECURSOR PROTEIN CLEAVING ENZYME 1, BETA-SITE APP CLEAVING ENZYME 1, COMPND 7 MEMAPSIN-2, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2; COMPND 8 EC: 3.4.23.46; COMPND 9 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: BACE1, BACE, KIAA1149; 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 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.V.EFREMOV,F.F.VAJDOS,K.BORZILLERI,S.CAPETTA,P.DORFF,J.DUTRA, AUTHOR 2 M.MANSOUR,C.OBORSKI,T.O'CONNELL,T.J.O'SULLIVAN,J.PANDIT,H.WANG, AUTHOR 3 J.WITHKA REVDAT 4 04-APR-18 3UDN 1 REMARK REVDAT 3 08-NOV-17 3UDN 1 REMARK REVDAT 2 19-JUN-13 3UDN 1 JRNL REVDAT 1 18-APR-12 3UDN 0 JRNL AUTH I.V.EFREMOV,F.F.VAJDOS,K.A.BORZILLERI,S.CAPETTA,H.CHEN, JRNL AUTH 2 P.H.DORFF,J.K.DUTRA,S.W.GOLDSTEIN,M.MANSOUR,A.MCCOLL, JRNL AUTH 3 S.NOELL,C.E.OBORSKI,T.N.O'CONNELL,T.J.O'SULLIVAN,J.PANDIT, JRNL AUTH 4 H.WANG,B.WEI,J.M.WITHKA JRNL TITL DISCOVERY AND OPTIMIZATION OF A NOVEL SPIROPYRROLIDINE JRNL TITL 2 INHIBITOR OF {BETA}-SECRETASE (BACE1) THROUGH FRAGMENT-BASED JRNL TITL 3 DRUG DESIGN. JRNL REF J.MED.CHEM. V. 55 9069 2012 JRNL REFN ISSN 0022-2623 JRNL PMID 22468999 JRNL DOI 10.1021/JM201715D REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.G.TOMASSELLI,D.J.PADDOCK,T.L.EMMONS,A.M.MILDNER,J.W.LEONE, REMARK 1 AUTH 2 J.M.LULL,J.I.CIALDELLA,D.B.PRINCE,H.D.FISCHER, REMARK 1 AUTH 3 R.L.HEINRIKSON,T.E.BENSON REMARK 1 TITL HIGH YIELD EXPRESSION OF HUMAN BACE CONSTRUCTS IN REMARK 1 TITL 2 ESCHERICHIA COLI FOR REFOLDING, PURIFICATION, AND HIGH REMARK 1 TITL 3 RESOLUTION DIFFRACTING CRYSTAL FORMS. REMARK 1 REF PROTEIN PEPT.LETT. V. 15 131 2008 REMARK 1 REFN ISSN 0929-8665 REMARK 1 PMID 18289105 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 19200 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 996 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1205 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3106 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.22000 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): 0.370 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.282 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.411 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3230 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4388 ; 1.378 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 7.724 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;35.776 ;23.826 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 507 ;15.983 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.170 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 473 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2507 ; 0.008 ; 0.021 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): 1955 ; 0.893 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3165 ; 1.626 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1275 ; 2.565 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1223 ; 3.995 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3UDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 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 FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19236 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.193 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 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: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN IN SODIUM BORATE, PH 8.5, REMARK 280 RESERVOIR: 30% PEG200, 0.1 M SODIUM ACETATE, PH 5.2-5.4, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 49.27400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.27400 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.21600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.69850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.21600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.69850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.27400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.21600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.69850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.27400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.21600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.69850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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 GLY A -3 REMARK 465 SER A -2 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 HIS A 399 REMARK 465 HIS A 400 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 O HOH A 405 O HOH A 602 1.53 REMARK 500 O HOH A 418 O HOH A 671 1.62 REMARK 500 O TYR A 71 OG1 THR A 72 1.72 REMARK 500 OD1 ASN A 278 O HOH A 645 1.76 REMARK 500 OD2 ASP A 311 OG1 THR A 314 1.85 REMARK 500 O HOH A 654 O HOH A 656 1.87 REMARK 500 O HOH A 454 O HOH A 665 1.93 REMARK 500 OE2 GLU A 125 O HOH A 454 2.03 REMARK 500 O HOH A 566 O HOH A 647 2.08 REMARK 500 O HOH A 624 O HOH A 672 2.12 REMARK 500 O HOH A 623 O HOH A 669 2.12 REMARK 500 OE1 GLU A 125 NH2 ARG A 195 2.16 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 THR A 72 -59.03 115.76 REMARK 500 LYS A 75 124.94 122.84 REMARK 500 HIS A 89 44.10 -100.06 REMARK 500 LEU A 149 142.11 -171.28 REMARK 500 TRP A 197 -80.78 -134.00 REMARK 500 ARG A 205 139.79 -175.13 REMARK 500 ASN A 293 -0.90 77.82 REMARK 500 ASP A 363 -166.65 -128.42 REMARK 500 MET A 379 129.55 -31.49 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 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 398 NE2 REMARK 620 2 HIS A 396 ND1 119.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 09B A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UDH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 1 REMARK 900 RELATED ID: 3UDJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 5 REMARK 900 RELATED ID: 3UDK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 6 REMARK 900 RELATED ID: 3UDM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 8 REMARK 900 RELATED ID: 3UDP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 12 REMARK 900 RELATED ID: 3UDQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 13 REMARK 900 RELATED ID: 3UDR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 14 REMARK 900 RELATED ID: 3UDY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACE WITH COMPOUND 11 DBREF 3UDN A -3 392 UNP P56817 BACE1_HUMAN 58 453 SEQADV 3UDN ARG A 393 UNP P56817 EXPRESSION TAG SEQADV 3UDN SER A 394 UNP P56817 EXPRESSION TAG SEQADV 3UDN HIS A 395 UNP P56817 EXPRESSION TAG SEQADV 3UDN HIS A 396 UNP P56817 EXPRESSION TAG SEQADV 3UDN HIS A 397 UNP P56817 EXPRESSION TAG SEQADV 3UDN HIS A 398 UNP P56817 EXPRESSION TAG SEQADV 3UDN HIS A 399 UNP P56817 EXPRESSION TAG SEQADV 3UDN HIS A 400 UNP P56817 EXPRESSION TAG SEQRES 1 A 404 GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY LYS SEQRES 2 A 404 SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY SER SEQRES 3 A 404 PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY SER SEQRES 4 A 404 SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE LEU SEQRES 5 A 404 HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR ARG SEQRES 6 A 404 ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN GLY SEQRES 7 A 404 LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER ILE SEQRES 8 A 404 PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE ALA SEQRES 9 A 404 ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY SER SEQRES 10 A 404 ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU ILE SEQRES 11 A 404 ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP SER SEQRES 12 A 404 LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER LEU SEQRES 13 A 404 GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER GLU SEQRES 14 A 404 VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY GLY SEQRES 15 A 404 ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR THR SEQRES 16 A 404 PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE VAL SEQRES 17 A 404 ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP CYS SEQRES 18 A 404 LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER GLY SEQRES 19 A 404 THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU ALA SEQRES 20 A 404 ALA VAL LYS SER ILE LYS ALA ALA SER SER THR GLU LYS SEQRES 21 A 404 PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL CYS SEQRES 22 A 404 TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO VAL SEQRES 23 A 404 ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN SER SEQRES 24 A 404 PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG PRO SEQRES 25 A 404 VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR LYS SEQRES 26 A 404 PHE ALA ILE SER GLN SER SER THR GLY THR VAL MET GLY SEQRES 27 A 404 ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP ARG SEQRES 28 A 404 ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS HIS SEQRES 29 A 404 VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY PRO SEQRES 30 A 404 PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN ILE SEQRES 31 A 404 PRO GLN THR ASP GLU SER ARG SER HIS HIS HIS HIS HIS SEQRES 32 A 404 HIS HET 09B A 401 26 HET EDO A 402 4 HET EDO A 403 4 HET PEG A 409 7 HET ZN A 404 1 HETNAM 09B 4-CYANOBENZYL (3S,5'R)-2-OXO-1,2-DIHYDROSPIRO[INDOLE-3, HETNAM 2 09B 3'-PYRROLIDINE]-5'-CARBOXYLATE HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 09B C20 H17 N3 O3 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 PEG C4 H10 O3 FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *268(H2 O) HELIX 1 1 GLN A 53 SER A 57 5 5 HELIX 2 2 TYR A 123 ALA A 127 5 5 HELIX 3 3 PRO A 135 THR A 144 1 10 HELIX 4 4 ASP A 180 SER A 182 5 3 HELIX 5 5 ASP A 216 TYR A 220 5 5 HELIX 6 6 LYS A 238 SER A 252 1 15 HELIX 7 7 PRO A 258 LEU A 263 1 6 HELIX 8 8 PRO A 276 PHE A 280 5 5 HELIX 9 9 LEU A 301 TYR A 305 1 5 HELIX 10 10 GLY A 334 GLU A 339 1 6 HELIX 11 11 THR A 389 HIS A 395 1 7 SHEET 1 A 9 ARG A 61 VAL A 69 0 SHEET 2 A 9 TRP A 76 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 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 5 A 9 SER A 169 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 VAL A 343 N LEU A 152 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 TRP A 189 O PHE A 354 SHEET 1 B13 ARG A 61 VAL A 69 0 SHEET 2 B13 TRP A 76 SER A 86 -1 O LEU A 80 N LYS A 65 SHEET 3 B13 VAL A 95 SER A 105 -1 O ILE A 99 N GLY A 81 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 VAL A 16 O ILE A 29 SHEET 8 B13 LEU A 6 LYS A 9 -1 N ARG A 7 O TYR A 15 SHEET 9 B13 SER A 169 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 VAL A 343 N LEU A 152 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 TRP A 189 O PHE A 354 SHEET 1 C 5 GLN A 211 ASP A 212 0 SHEET 2 C 5 ILE A 203 ILE A 208 -1 N ILE A 208 O GLN A 211 SHEET 3 C 5 ILE A 283 MET A 288 -1 O TYR A 286 N ARG A 205 SHEET 4 C 5 GLN A 294 ILE A 300 -1 O PHE A 296 N LEU A 287 SHEET 5 C 5 ALA A 369 VAL A 375 -1 O GLU A 371 N ARG A 297 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 234 SHEET 1 E 3 VAL A 268 GLN A 271 0 SHEET 2 E 3 ASP A 317 PHE A 322 -1 O ASP A 318 N TRP A 270 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 2.02 SSBOND 2 CYS A 217 CYS A 382 1555 1555 2.05 SSBOND 3 CYS A 269 CYS A 319 1555 1555 2.04 LINK NE2 HIS A 398 ZN ZN A 404 1555 1555 1.99 LINK ND1 HIS A 396 ZN ZN A 404 1555 1555 2.11 CISPEP 1 SER A 22 PRO A 23 0 -2.03 CISPEP 2 ARG A 128 PRO A 129 0 1.92 CISPEP 3 TYR A 222 ASP A 223 0 3.62 CISPEP 4 GLY A 372 PRO A 373 0 -4.00 SITE 1 AC1 11 LEU A 30 ASP A 32 GLY A 34 PRO A 70 SITE 2 AC1 11 TYR A 71 GLN A 73 PHE A 108 ARG A 128 SITE 3 AC1 11 TYR A 198 ASP A 228 GLY A 230 SITE 1 AC2 4 ARG A 96 ASN A 98 GLU A 134 SER A 139 SITE 1 AC3 1 TYR A 384 SITE 1 AC4 9 GLN A 12 GLY A 13 SER A 229 GLY A 230 SITE 2 AC4 9 THR A 231 THR A 232 ALA A 335 HOH A 495 SITE 3 AC4 9 HOH A 571 SITE 1 AC5 4 GLU A 255 ASP A 390 HIS A 396 HIS A 398 CRYST1 74.432 103.397 98.548 90.00 90.00 90.00 C 2 2 21 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 0.013435 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010147 0.00000