HEADER HYDROLASE 27-NOV-15 5F01
TITLE CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH (1SR,2SR)-2-((R)-2-AMINO-
TITLE 2 5,5-DIFLUORO-4-METHYL-5,6-DIHYDRO-4H-1,3-OXAZIN-4-YL)-N-(3-
TITLE 3 CHLOROQUINOLIN-8-YL)CYCLOPROPANECARBOXAMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-SECRETASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ASPARTYL PROTEASE 2,ASP 2,BETA-SITE AMYLOID PRECURSOR
COMPND 5 PROTEIN CLEAVING ENZYME 1,BETA-SITE APP CLEAVING ENZYME 1,MEMAPSIN-2,
COMPND 6 MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2;
COMPND 7 EC: 3.4.23.46;
COMPND 8 ENGINEERED: YES;
COMPND 9 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, BACE, KIAA1149;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PROTEASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.BANNER,J.BENZ,M.STIHLE,A.KUGLSTATTER
REVDAT 3 29-NOV-17 5F01 1 REMARK
REVDAT 2 25-MAY-16 5F01 1 JRNL
REVDAT 1 24-FEB-16 5F01 0
JRNL AUTH B.KUHN,W.GUBA,J.HERT,D.BANNER,C.BISSANTZ,S.CECCARELLI,
JRNL AUTH 2 W.HAAP,M.KORNER,A.KUGLSTATTER,C.LERNER,P.MATTEI,W.NEIDHART,
JRNL AUTH 3 E.PINARD,M.G.RUDOLPH,T.SCHULZ-GASCH,T.WOLTERING,M.STAHL
JRNL TITL A REAL-WORLD PERSPECTIVE ON MOLECULAR DESIGN.
JRNL REF J.MED.CHEM. V. 59 4087 2016
JRNL REFN ISSN 0022-2623
JRNL PMID 26878596
JRNL DOI 10.1021/ACS.JMEDCHEM.5B01875
REMARK 2
REMARK 2 RESOLUTION. 1.52 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0077
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.78
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 3 NUMBER OF REFLECTIONS : 75036
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) : 0.187
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 4011
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) : 1.52
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.56
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5096
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.63
REMARK 3 BIN R VALUE (WORKING SET) : 0.3270
REMARK 3 BIN FREE R VALUE SET COUNT : 279
REMARK 3 BIN FREE R VALUE : 0.3650
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3009
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 47
REMARK 3 SOLVENT ATOMS : 409
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.81
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.07000
REMARK 3 B22 (A**2) : -0.07000
REMARK 3 B33 (A**2) : 0.11000
REMARK 3 B12 (A**2) : -0.04000
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): 0.071
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.401
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3287 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4500 ; 1.296 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 6.353 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;34.394 ;23.444
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 532 ;12.480 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;14.024 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 492 ; 0.086 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2549 ; 0.006 ; 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): 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 : 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: HYDROGENS HAVE BEEN USED IF PRESENT IN
REMARK 3 THE INPUT
REMARK 4
REMARK 4 5F01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-15.
REMARK 100 THE DEPOSITION ID IS D_1000215780.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-JUN-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75036
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520
REMARK 200 RESOLUTION RANGE LOW (A) : 47.780
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 12.81
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.03930
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 12.45
REMARK 200 R MERGE FOR SHELL (I) : 0.54830
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.830
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: IN-HOUSE STRUCTURE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 59.23
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M SODIUM FORMATE, 100MM HEPES, PH
REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
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 56.72067
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 113.44133
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 85.08100
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 141.80167
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 28.36033
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 56.72067
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 113.44133
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 141.80167
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 85.08100
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 28.36033
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1100 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 604 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 694 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 976 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 LEU A 222
REMARK 465 ASN A 223
REMARK 465 GLN A 224
REMARK 465 SER A 225
REMARK 465 GLU A 226
REMARK 465 VAL A 227
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 ASP A 372 CG OD1 OD2
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 A 150 54.39 -97.41
REMARK 500 TRP A 258 -85.41 -139.53
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 NA A 502 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 VAL A 202 O
REMARK 620 2 THR A 205 O 85.1
REMARK 620 3 HOH A 799 O 163.2 80.8
REMARK 620 4 HOH A 675 O 100.5 98.7 90.5
REMARK 620 5 HOH A 869 O 91.9 80.1 76.9 167.4
REMARK 620 6 HOH A 938 O 90.7 165.7 100.8 95.5 86.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 501 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 242 O
REMARK 620 2 TYR A 245 O 84.0
REMARK 620 3 HOH A 937 O 84.7 163.0
REMARK 620 4 HOH A 767 O 150.6 101.0 95.0
REMARK 620 5 HOH A 906 O 99.4 80.3 89.1 109.9
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 NA A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5T7 A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 507
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5EZX RELATED DB: PDB
REMARK 900 RELATED ID: 5EZZ RELATED DB: PDB
REMARK 900 RELATED ID: 5F00 RELATED DB: PDB
DBREF 5F01 A 57 446 UNP P56817 BACE1_HUMAN 57 446
SEQADV 5F01 ALA A 307 UNP P56817 LYS 307 ENGINEERED MUTATION
SEQRES 1 A 390 ARG GLY SER PHE VAL GLU MET VAL ASP ASN LEU ARG GLY
SEQRES 2 A 390 LYS SER GLY GLN GLY TYR TYR VAL GLU MET THR VAL GLY
SEQRES 3 A 390 SER PRO PRO GLN THR LEU ASN ILE LEU VAL ASP THR GLY
SEQRES 4 A 390 SER SER ASN PHE ALA VAL GLY ALA ALA PRO HIS PRO PHE
SEQRES 5 A 390 LEU HIS ARG TYR TYR GLN ARG GLN LEU SER SER THR TYR
SEQRES 6 A 390 ARG ASP LEU ARG LYS GLY VAL TYR VAL PRO TYR THR GLN
SEQRES 7 A 390 GLY LYS TRP GLU GLY GLU LEU GLY THR ASP LEU VAL SER
SEQRES 8 A 390 ILE PRO HIS GLY PRO ASN VAL THR VAL ARG ALA ASN ILE
SEQRES 9 A 390 ALA ALA ILE THR GLU SER ASP LYS PHE PHE ILE ASN GLY
SEQRES 10 A 390 SER ASN TRP GLU GLY ILE LEU GLY LEU ALA TYR ALA GLU
SEQRES 11 A 390 ILE ALA ARG PRO ASP ASP SER LEU GLU PRO PHE PHE ASP
SEQRES 12 A 390 SER LEU VAL LYS GLN THR HIS VAL PRO ASN LEU PHE SER
SEQRES 13 A 390 LEU GLN LEU CYS GLY ALA GLY PHE PRO LEU ASN GLN SER
SEQRES 14 A 390 GLU VAL LEU ALA SER VAL GLY GLY SER MET ILE ILE GLY
SEQRES 15 A 390 GLY ILE ASP HIS SER LEU TYR THR GLY SER LEU TRP TYR
SEQRES 16 A 390 THR PRO ILE ARG ARG GLU TRP TYR TYR GLU VAL ILE ILE
SEQRES 17 A 390 VAL ARG VAL GLU ILE ASN GLY GLN ASP LEU LYS MET ASP
SEQRES 18 A 390 CYS LYS GLU TYR ASN TYR ASP LYS SER ILE VAL ASP SER
SEQRES 19 A 390 GLY THR THR ASN LEU ARG LEU PRO LYS LYS VAL PHE GLU
SEQRES 20 A 390 ALA ALA VAL ALA SER ILE LYS ALA ALA SER SER THR GLU
SEQRES 21 A 390 LYS PHE PRO ASP GLY PHE TRP LEU GLY GLU GLN LEU VAL
SEQRES 22 A 390 CYS TRP GLN ALA GLY THR THR PRO TRP ASN ILE PHE PRO
SEQRES 23 A 390 VAL ILE SER LEU TYR LEU MET GLY GLU VAL THR ASN GLN
SEQRES 24 A 390 SER PHE ARG ILE THR ILE LEU PRO GLN GLN TYR LEU ARG
SEQRES 25 A 390 PRO VAL GLU ASP VAL ALA THR SER GLN ASP ASP CYS TYR
SEQRES 26 A 390 LYS PHE ALA ILE SER GLN SER SER THR GLY THR VAL MET
SEQRES 27 A 390 GLY ALA VAL ILE MET GLU GLY PHE TYR VAL VAL PHE ASP
SEQRES 28 A 390 ARG ALA ARG LYS ARG ILE GLY PHE ALA VAL SER ALA CYS
SEQRES 29 A 390 HIS VAL HIS ASP GLU PHE ARG THR ALA ALA VAL GLU GLY
SEQRES 30 A 390 PRO PHE VAL THR LEU ASP MET GLU ASP CYS GLY TYR ASN
HET NA A 501 1
HET NA A 502 1
HET DMS A 503 4
HET 5T7 A 504 27
HET DMS A 505 4
HET GOL A 506 6
HET ACT A 507 4
HETNAM NA SODIUM ION
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM 5T7 (1~{R},2~{R})-2-[(4~{R})-2-AZANYL-5,5-BIS(FLUORANYL)-4-
HETNAM 2 5T7 METHYL-6~{H}-1,3-OXAZIN-4-YL]-~{N}-(3-
HETNAM 3 5T7 CHLORANYLQUINOLIN-8-YL)CYCLOPROPANE-1-CARBOXAMIDE
HETNAM GOL GLYCEROL
HETNAM ACT ACETATE ION
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 NA 2(NA 1+)
FORMUL 4 DMS 2(C2 H6 O S)
FORMUL 5 5T7 C18 H17 CL F2 N4 O2
FORMUL 7 GOL C3 H8 O3
FORMUL 8 ACT C2 H3 O2 1-
FORMUL 9 HOH *409(H2 O)
HELIX 1 AA1 GLN A 114 SER A 118 5 5
HELIX 2 AA2 TYR A 184 ALA A 188 5 5
HELIX 3 AA3 PRO A 196 THR A 205 1 10
HELIX 4 AA4 ASP A 241 SER A 243 5 3
HELIX 5 AA5 ASP A 277 TYR A 283 5 7
HELIX 6 AA6 LYS A 299 SER A 313 1 15
HELIX 7 AA7 PRO A 319 LEU A 324 1 6
HELIX 8 AA8 PRO A 337 PHE A 341 5 5
HELIX 9 AA9 LEU A 362 TYR A 366 1 5
HELIX 10 AB1 GLY A 395 GLU A 400 1 6
HELIX 11 AB2 ARG A 408 ARG A 410 5 3
HELIX 12 AB3 ASP A 439 GLY A 444 5 6
SHEET 1 AA1 9 ARG A 122 PRO A 131 0
SHEET 2 AA1 9 LYS A 136 SER A 147 -1 O TRP A 137 N VAL A 130
SHEET 3 AA1 9 TYR A 75 VAL A 81 -1 N THR A 80 O SER A 147
SHEET 4 AA1 9 LEU A 67 GLY A 69 -1 N ARG A 68 O TYR A 76
SHEET 5 AA1 9 VAL A 231 ILE A 237 -1 O GLY A 233 N LEU A 67
SHEET 6 AA1 9 PHE A 211 CYS A 216 -1 N CYS A 216 O GLY A 232
SHEET 7 AA1 9 PHE A 402 ASP A 407 -1 O VAL A 404 N LEU A 213
SHEET 8 AA1 9 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403
SHEET 9 AA1 9 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413
SHEET 1 AA213 ARG A 122 PRO A 131 0
SHEET 2 AA213 LYS A 136 SER A 147 -1 O TRP A 137 N VAL A 130
SHEET 3 AA213 VAL A 156 ASP A 167 -1 O ALA A 162 N GLU A 140
SHEET 4 AA213 PHE A 99 GLY A 102 1 N VAL A 101 O ILE A 163
SHEET 5 AA213 GLY A 178 GLY A 181 -1 O ILE A 179 N ALA A 100
SHEET 6 AA213 GLN A 86 ASP A 93 1 N LEU A 91 O LEU A 180
SHEET 7 AA213 TYR A 75 VAL A 81 -1 N TYR A 75 O VAL A 92
SHEET 8 AA213 LEU A 67 GLY A 69 -1 N ARG A 68 O TYR A 76
SHEET 9 AA213 VAL A 231 ILE A 237 -1 O GLY A 233 N LEU A 67
SHEET 10 AA213 PHE A 211 CYS A 216 -1 N CYS A 216 O GLY A 232
SHEET 11 AA213 PHE A 402 ASP A 407 -1 O VAL A 404 N LEU A 213
SHEET 12 AA213 ARG A 412 SER A 418 -1 O ALA A 416 N TYR A 403
SHEET 13 AA213 TYR A 245 PRO A 253 -1 N THR A 252 O ILE A 413
SHEET 1 AA3 5 GLU A 261 VAL A 262 0
SHEET 2 AA3 5 SER A 286 VAL A 288 -1 O SER A 286 N VAL A 262
SHEET 3 AA3 5 THR A 392 MET A 394 1 O MET A 394 N ILE A 287
SHEET 4 AA3 5 LEU A 295 PRO A 298 -1 N ARG A 296 O VAL A 393
SHEET 5 AA3 5 ILE A 385 SER A 388 1 O SER A 386 N LEU A 297
SHEET 1 AA4 5 GLN A 272 ASP A 273 0
SHEET 2 AA4 5 ILE A 264 ILE A 269 -1 N ILE A 269 O GLN A 272
SHEET 3 AA4 5 ILE A 344 MET A 349 -1 O TYR A 347 N ARG A 266
SHEET 4 AA4 5 GLN A 355 ILE A 361 -1 O ILE A 359 N LEU A 346
SHEET 5 AA4 5 ALA A 430 VAL A 436 -1 O GLU A 432 N ARG A 358
SHEET 1 AA5 3 VAL A 329 TRP A 331 0
SHEET 2 AA5 3 ASP A 379 PHE A 383 -1 O TYR A 381 N VAL A 329
SHEET 3 AA5 3 LEU A 367 VAL A 370 -1 N ARG A 368 O LYS A 382
SSBOND 1 CYS A 216 CYS A 420 1555 1555 2.06
SSBOND 2 CYS A 278 CYS A 443 1555 1555 2.04
SSBOND 3 CYS A 330 CYS A 380 1555 1555 2.05
LINK O VAL A 202 NA NA A 502 1555 1555 2.32
LINK O THR A 205 NA NA A 502 1555 1555 2.41
LINK O HIS A 242 NA NA A 501 1555 1555 2.50
LINK O TYR A 245 NA NA A 501 1555 1555 2.32
LINK NA NA A 501 O HOH A 937 1555 1555 2.37
LINK NA NA A 501 O HOH A 767 1555 1555 2.36
LINK NA NA A 501 O HOH A 906 1555 1555 2.41
LINK NA NA A 502 O HOH A 799 1555 1555 2.42
LINK NA NA A 502 O HOH A 675 1555 1555 2.38
LINK NA NA A 502 O HOH A 869 1555 1555 2.46
LINK NA NA A 502 O HOH A 938 1555 1555 2.36
CISPEP 1 SER A 83 PRO A 84 0 0.09
CISPEP 2 ARG A 189 PRO A 190 0 7.88
CISPEP 3 PHE A 220 PRO A 221 0 -1.78
CISPEP 4 TYR A 283 ASP A 284 0 1.41
CISPEP 5 GLY A 433 PRO A 434 0 -6.35
SITE 1 AC1 5 HIS A 242 TYR A 245 HOH A 767 HOH A 906
SITE 2 AC1 5 HOH A 937
SITE 1 AC2 6 VAL A 202 THR A 205 HOH A 675 HOH A 799
SITE 2 AC2 6 HOH A 869 HOH A 938
SITE 1 AC3 4 ARG A 157 ASN A 159 GLU A 195 HOH A 814
SITE 1 AC4 14 GLY A 72 GLY A 74 LEU A 91 ASP A 93
SITE 2 AC4 14 TYR A 132 ILE A 171 ASP A 289 SER A 290
SITE 3 AC4 14 GLY A 291 THR A 292 THR A 293 ALA A 396
SITE 4 AC4 14 ACT A 507 HOH A 617
SITE 1 AC5 3 LYS A 279 GLU A 280 LYS A 300
SITE 1 AC6 10 HIS A 106 PHE A 108 SER A 166 ASP A 167
SITE 2 AC6 10 LYS A 168 ILE A 171 ASN A 172 HOH A 604
SITE 3 AC6 10 HOH A 605 HOH A 680
SITE 1 AC7 11 LYS A 70 SER A 71 GLY A 72 GLN A 73
SITE 2 AC7 11 GLY A 74 TYR A 75 VAL A 231 ARG A 368
SITE 3 AC7 11 5T7 A 504 HOH A 621 HOH A 686
CRYST1 102.413 102.413 170.162 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 0.009764 0.005637 0.000000 0.00000
SCALE2 0.000000 0.011275 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005877 0.00000
(ATOM LINES ARE NOT SHOWN.)
END