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HEADER HYDROLASE 20-FEB-20 6M07
TITLE CRYSTAL STRUCTURE OF LP-PLA2 IN COMPLEX WITH A NOVEL COVALENT
TITLE 2 INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: PAF ACETYLHYDROLASE,1-ALKYL-2-ACETYLGLYCEROPHOSPHOCHOLINE
COMPND 5 ESTERASE,2-ACETYL-1-ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE,GROUP-VIIA
COMPND 6 PHOSPHOLIPASE A2,GVIIA-PLA2,LDL-ASSOCIATED PHOSPHOLIPASE A2,LDL-
COMPND 7 PLA(2),PAF 2-ACYLHYDROLASE;
COMPND 8 EC: 3.1.1.47;
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: PLA2G7, PAFAH;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)
KEYWDS LP-PLA2, COVALENT INHIBITOR, COMPLEX STRUCTURE, SERINE
KEYWDS 2 PHOSPHOLIPASE., HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.C.HU,Y.C.XU
REVDAT 2 13-JAN-21 6M07 1 COMPND HETNAM FORMUL
REVDAT 1 30-DEC-20 6M07 0
JRNL AUTH F.HUANG,H.HU,K.WANG,C.PENG,W.XU,Y.ZHANG,J.GAO,Y.LIU,H.ZHOU,
JRNL AUTH 2 R.HUANG,M.LI,J.SHEN,Y.XU
JRNL TITL IDENTIFICATION OF HIGHLY SELECTIVE LIPOPROTEIN-ASSOCIATED
JRNL TITL 2 PHOSPHOLIPASE A2 (LP-PLA2) INHIBITORS BY A COVALENT
JRNL TITL 3 FRAGMENT-BASED APPROACH.
JRNL REF J.MED.CHEM. V. 63 7052 2020
JRNL REFN ISSN 0022-2623
JRNL PMID 32459096
JRNL DOI 10.1021/ACS.JMEDCHEM.0C00372
REMARK 2
REMARK 2 RESOLUTION. 2.64 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0232
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.64
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.95
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 87.5
REMARK 3 NUMBER OF REFLECTIONS : 18126
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) : 0.203
REMARK 3 R VALUE (WORKING SET) : 0.200
REMARK 3 FREE R VALUE : 0.249
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 934
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) : 2.65
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71
REMARK 3 REFLECTION IN BIN (WORKING SET) : 501
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 33.48
REMARK 3 BIN R VALUE (WORKING SET) : 0.2220
REMARK 3 BIN FREE R VALUE SET COUNT : 28
REMARK 3 BIN FREE R VALUE : 0.3870
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5655
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 86
REMARK 3 SOLVENT ATOMS : 8
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.38
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.46000
REMARK 3 B22 (A**2) : -0.82000
REMARK 3 B33 (A**2) : 0.55000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.51000
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): 0.394
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.294
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.103
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5891 ; 0.008 ; 0.013
REMARK 3 BOND LENGTHS OTHERS (A): 5159 ; 0.001 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8017 ; 1.689 ; 1.656
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11888 ; 1.290 ; 1.591
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 736 ; 8.048 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 298 ;35.907 ;22.013
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 875 ;16.653 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.247 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 780 ; 0.067 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6744 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1324 ; 0.003 ; 0.020
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 : NULL
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 ADDED IN THE RIDING
REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 6M07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-20.
REMARK 100 THE DEPOSITION ID IS D_1300015779.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-DEC-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL18U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.979
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 : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21641
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.640
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 (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.200
REMARK 200 R MERGE (I) : 0.20000
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 4.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4
REMARK 200 DATA REDUNDANCY IN SHELL : 4.20
REMARK 200 R MERGE FOR SHELL (I) : 1.30600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 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: PHASER
REMARK 200 STARTING MODEL: 5I9I
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.90
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MOPS PH 6.6, 0.4 M LI2SO4, 22.5
REMARK 280 -27% (W/V) (NH4)2SO4, 1 M NA-AC, 1.4 % 1,4-BUTANEDIOL, 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 56.34350
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.92850
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.34350
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.92850
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: 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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 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 THR A 54 OG1 CG2
REMARK 470 LYS A 55 CG CD CE NZ
REMARK 470 SER A 64 OG
REMARK 470 LYS A 77 CD CE NZ
REMARK 470 GLN A 88 CG CD OE1 NE2
REMARK 470 ASP A 89 CG OD1 OD2
REMARK 470 ARG A 92 CD NE CZ NH1 NH2
REMARK 470 LEU A 96 CD1
REMARK 470 LYS A 101 CG CD CE NZ
REMARK 470 LYS A 109 CG CD CE NZ
REMARK 470 LEU A 111 CD1 CD2
REMARK 470 THR A 113 OG1 CG2
REMARK 470 HIS A 114 CG ND1 CD2 CE1 NE2
REMARK 470 TRP A 115 CG CD1 CD2 NE1 CE2 CE3 CZ2
REMARK 470 TRP A 115 CZ3 CH2
REMARK 470 LEU A 116 CG CD1 CD2
REMARK 470 LEU A 123 CG CD1 CD2
REMARK 470 LYS A 143 CE NZ
REMARK 470 GLN A 193 CD OE1 NE2
REMARK 470 LEU A 204 CD1 CD2
REMARK 470 LYS A 210 CG CD CE NZ
REMARK 470 GLN A 211 CG CD OE1 NE2
REMARK 470 GLU A 212 CG CD OE1 OE2
REMARK 470 ILE A 217 CD1
REMARK 470 GLU A 220 CD OE1 OE2
REMARK 470 LYS A 227 CD CE NZ
REMARK 470 LYS A 243 CE NZ
REMARK 470 LYS A 246 CG CD CE NZ
REMARK 470 LYS A 252 CG CD CE NZ
REMARK 470 GLU A 256 CG CD OE1 OE2
REMARK 470 LYS A 259 CE NZ
REMARK 470 GLU A 285 CG CD OE1 OE2
REMARK 470 GLN A 287 OE1 NE2
REMARK 470 ASP A 304 CG OD1 OD2
REMARK 470 SER A 308 OG
REMARK 470 ILE A 329 CD1
REMARK 470 LYS A 333 CD CE NZ
REMARK 470 LYS A 363 CG CD CE NZ
REMARK 470 ILE A 364 CG1 CG2 CD1
REMARK 470 MET A 368 CG SD CE
REMARK 470 LYS A 370 CG CD CE NZ
REMARK 470 LYS A 394 CG CD CE NZ
REMARK 470 LYS A 400 CG CD CE NZ
REMARK 470 ASP A 401 CG OD1 OD2
REMARK 470 THR B 54 OG1 CG2
REMARK 470 LYS B 55 CG CD CE NZ
REMARK 470 SER B 64 OG
REMARK 470 LYS B 77 CD CE NZ
REMARK 470 GLN B 88 CG CD OE1 NE2
REMARK 470 ASP B 89 CG OD1 OD2
REMARK 470 ARG B 92 CD NE CZ NH1 NH2
REMARK 470 LEU B 96 CD1
REMARK 470 LYS B 101 CG CD CE NZ
REMARK 470 LYS B 109 CG CD CE NZ
REMARK 470 LEU B 111 CD1 CD2
REMARK 470 THR B 113 OG1 CG2
REMARK 470 HIS B 114 CG ND1 CD2 CE1 NE2
REMARK 470 TRP B 115 CG CD1 CD2 NE1 CE2 CE3 CZ2
REMARK 470 TRP B 115 CZ3 CH2
REMARK 470 LEU B 116 CG CD1 CD2
REMARK 470 LEU B 123 CG CD1 CD2
REMARK 470 LYS B 143 CE NZ
REMARK 470 GLN B 193 CD OE1 NE2
REMARK 470 LEU B 204 CD1 CD2
REMARK 470 LYS B 210 CG CD CE NZ
REMARK 470 GLN B 211 CG CD OE1 NE2
REMARK 470 GLU B 212 CG CD OE1 OE2
REMARK 470 ILE B 217 CD1
REMARK 470 GLU B 220 CD OE1 OE2
REMARK 470 LYS B 227 CD CE NZ
REMARK 470 LYS B 243 CE NZ
REMARK 470 LYS B 246 CG CD CE NZ
REMARK 470 LYS B 252 CG CD CE NZ
REMARK 470 GLU B 256 CG CD OE1 OE2
REMARK 470 LYS B 259 CE NZ
REMARK 470 GLU B 285 CG CD OE1 OE2
REMARK 470 GLN B 287 OE1 NE2
REMARK 470 ASP B 304 CG OD1 OD2
REMARK 470 ILE B 329 CD1
REMARK 470 LYS B 333 CD CE NZ
REMARK 470 LYS B 363 CG CD CE NZ
REMARK 470 ILE B 364 CG1 CG2 CD1
REMARK 470 MET B 368 CG SD CE
REMARK 470 LYS B 370 CG CD CE NZ
REMARK 470 LYS B 394 CG CD CE NZ
REMARK 470 LYS B 400 CG CD CE NZ
REMARK 470 ASP B 401 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 PHE A 72 126.10 -177.01
REMARK 500 GLN A 88 -78.80 -64.96
REMARK 500 ASP A 91 38.55 -148.03
REMARK 500 TRP A 115 -33.55 -37.61
REMARK 500 LEU A 116 -75.13 -61.58
REMARK 500 ASP A 200 85.33 -69.44
REMARK 500 LEU A 206 129.50 -35.42
REMARK 500 ASP A 260 66.00 26.60
REMARK 500 SER A 273 -115.96 62.82
REMARK 500 ARG A 309 47.91 -103.19
REMARK 500 PRO A 313 150.72 -48.87
REMARK 500 LYS A 363 -80.03 -46.35
REMARK 500 ASP B 73 -177.32 -68.39
REMARK 500 ALA B 155 -163.68 -107.61
REMARK 500 ARG B 180 41.52 -100.13
REMARK 500 GLN B 211 -39.66 -37.38
REMARK 500 SER B 273 -102.58 77.91
REMARK 500 SER B 336 142.43 -171.41
REMARK 500 ASP B 403 1.29 -61.96
REMARK 500 ASP B 412 78.34 -101.23
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 BWO A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BWO B 501 and SER B
REMARK 800 273
DBREF 6M07 A 54 422 UNP Q13093 PAFA_HUMAN 54 422
DBREF 6M07 B 54 422 UNP Q13093 PAFA_HUMAN 54 422
SEQRES 1 A 369 THR LYS ILE PRO ARG GLY ASN GLY PRO TYR SER VAL GLY
SEQRES 2 A 369 CYS THR ASP LEU MET PHE ASP HIS THR ASN LYS GLY THR
SEQRES 3 A 369 PHE LEU ARG LEU TYR TYR PRO SER GLN ASP ASN ASP ARG
SEQRES 4 A 369 LEU ASP THR LEU TRP ILE PRO ASN LYS GLU TYR PHE TRP
SEQRES 5 A 369 GLY LEU SER LYS PHE LEU GLY THR HIS TRP LEU MET GLY
SEQRES 6 A 369 ASN ILE LEU ARG LEU LEU PHE GLY SER MET THR THR PRO
SEQRES 7 A 369 ALA ASN TRP ASN SER PRO LEU ARG PRO GLY GLU LYS TYR
SEQRES 8 A 369 PRO LEU VAL VAL PHE SER HIS GLY LEU GLY ALA PHE ARG
SEQRES 9 A 369 THR LEU TYR SER ALA ILE GLY ILE ASP LEU ALA SER HIS
SEQRES 10 A 369 GLY PHE ILE VAL ALA ALA VAL GLU HIS ARG ASP ARG SER
SEQRES 11 A 369 ALA SER ALA THR TYR TYR PHE LYS ASP GLN SER ALA ALA
SEQRES 12 A 369 GLU ILE GLY ASP LYS SER TRP LEU TYR LEU ARG THR LEU
SEQRES 13 A 369 LYS GLN GLU GLU GLU THR HIS ILE ARG ASN GLU GLN VAL
SEQRES 14 A 369 ARG GLN ARG ALA LYS GLU CYS SER GLN ALA LEU SER LEU
SEQRES 15 A 369 ILE LEU ASP ILE ASP HIS GLY LYS PRO VAL LYS ASN ALA
SEQRES 16 A 369 LEU ASP LEU LYS PHE ASP MET GLU GLN LEU LYS ASP SER
SEQRES 17 A 369 ILE ASP ARG GLU LYS ILE ALA VAL ILE GLY HIS SER PHE
SEQRES 18 A 369 GLY GLY ALA THR VAL ILE GLN THR LEU SER GLU ASP GLN
SEQRES 19 A 369 ARG PHE ARG CYS GLY ILE ALA LEU ASP ALA TRP MET PHE
SEQRES 20 A 369 PRO LEU GLY ASP GLU VAL TYR SER ARG ILE PRO GLN PRO
SEQRES 21 A 369 LEU PHE PHE ILE ASN SER GLU TYR PHE GLN TYR PRO ALA
SEQRES 22 A 369 ASN ILE ILE LYS MET LYS LYS CYS TYR SER PRO ASP LYS
SEQRES 23 A 369 GLU ARG LYS MET ILE THR ILE ARG GLY SER VAL HIS GLN
SEQRES 24 A 369 ASN PHE ALA ASP PHE THR PHE ALA THR GLY LYS ILE ILE
SEQRES 25 A 369 GLY HIS MET LEU LYS LEU LYS GLY ASP ILE ASP SER ASN
SEQRES 26 A 369 VAL ALA ILE ASP LEU SER ASN LYS ALA SER LEU ALA PHE
SEQRES 27 A 369 LEU GLN LYS HIS LEU GLY LEU HIS LYS ASP PHE ASP GLN
SEQRES 28 A 369 TRP ASP CYS LEU ILE GLU GLY ASP ASP GLU ASN LEU ILE
SEQRES 29 A 369 PRO GLY THR ASN ILE
SEQRES 1 B 369 THR LYS ILE PRO ARG GLY ASN GLY PRO TYR SER VAL GLY
SEQRES 2 B 369 CYS THR ASP LEU MET PHE ASP HIS THR ASN LYS GLY THR
SEQRES 3 B 369 PHE LEU ARG LEU TYR TYR PRO SER GLN ASP ASN ASP ARG
SEQRES 4 B 369 LEU ASP THR LEU TRP ILE PRO ASN LYS GLU TYR PHE TRP
SEQRES 5 B 369 GLY LEU SER LYS PHE LEU GLY THR HIS TRP LEU MET GLY
SEQRES 6 B 369 ASN ILE LEU ARG LEU LEU PHE GLY SER MET THR THR PRO
SEQRES 7 B 369 ALA ASN TRP ASN SER PRO LEU ARG PRO GLY GLU LYS TYR
SEQRES 8 B 369 PRO LEU VAL VAL PHE SER HIS GLY LEU GLY ALA PHE ARG
SEQRES 9 B 369 THR LEU TYR SER ALA ILE GLY ILE ASP LEU ALA SER HIS
SEQRES 10 B 369 GLY PHE ILE VAL ALA ALA VAL GLU HIS ARG ASP ARG SER
SEQRES 11 B 369 ALA SER ALA THR TYR TYR PHE LYS ASP GLN SER ALA ALA
SEQRES 12 B 369 GLU ILE GLY ASP LYS SER TRP LEU TYR LEU ARG THR LEU
SEQRES 13 B 369 LYS GLN GLU GLU GLU THR HIS ILE ARG ASN GLU GLN VAL
SEQRES 14 B 369 ARG GLN ARG ALA LYS GLU CYS SER GLN ALA LEU SER LEU
SEQRES 15 B 369 ILE LEU ASP ILE ASP HIS GLY LYS PRO VAL LYS ASN ALA
SEQRES 16 B 369 LEU ASP LEU LYS PHE ASP MET GLU GLN LEU LYS ASP SER
SEQRES 17 B 369 ILE ASP ARG GLU LYS ILE ALA VAL ILE GLY HIS SER PHE
SEQRES 18 B 369 GLY GLY ALA THR VAL ILE GLN THR LEU SER GLU ASP GLN
SEQRES 19 B 369 ARG PHE ARG CYS GLY ILE ALA LEU ASP ALA TRP MET PHE
SEQRES 20 B 369 PRO LEU GLY ASP GLU VAL TYR SER ARG ILE PRO GLN PRO
SEQRES 21 B 369 LEU PHE PHE ILE ASN SER GLU TYR PHE GLN TYR PRO ALA
SEQRES 22 B 369 ASN ILE ILE LYS MET LYS LYS CYS TYR SER PRO ASP LYS
SEQRES 23 B 369 GLU ARG LYS MET ILE THR ILE ARG GLY SER VAL HIS GLN
SEQRES 24 B 369 ASN PHE ALA ASP PHE THR PHE ALA THR GLY LYS ILE ILE
SEQRES 25 B 369 GLY HIS MET LEU LYS LEU LYS GLY ASP ILE ASP SER ASN
SEQRES 26 B 369 VAL ALA ILE ASP LEU SER ASN LYS ALA SER LEU ALA PHE
SEQRES 27 B 369 LEU GLN LYS HIS LEU GLY LEU HIS LYS ASP PHE ASP GLN
SEQRES 28 B 369 TRP ASP CYS LEU ILE GLU GLY ASP ASP GLU ASN LEU ILE
SEQRES 29 B 369 PRO GLY THR ASN ILE
HET BWO A 501 43
HET BWO B 501 43
HETNAM BWO (2S)-2-[(E)-3-[2-(DIETHYLAMINO)ETHYL-[[4-[4-
HETNAM 2 BWO (TRIFLUOROMETHYL)-2-[2,2,2-TRIS(FLUORANYL)
HETNAM 3 BWO ETHOXY]PHENYL]PHENYL]METHYL]AMINO]-1-OXIDANYL-3-
HETNAM 4 BWO OXIDANYLIDENE-PROP-1-ENYL]PYRROLIDINE-1-CARBOXYLIC
HETNAM 5 BWO ACID
FORMUL 3 BWO 2(C30 H35 F6 N3 O5)
FORMUL 5 HOH *8(H2 O)
HELIX 1 AA1 ASN A 100 GLY A 112 1 13
HELIX 2 AA2 LEU A 116 GLY A 126 1 11
HELIX 3 AA3 TYR A 160 SER A 169 1 10
HELIX 4 AA4 ASP A 192 GLY A 199 1 8
HELIX 5 AA5 GLU A 213 HIS A 241 1 29
HELIX 6 AA6 ASP A 254 LYS A 259 5 6
HELIX 7 AA7 SER A 273 ASP A 286 1 14
HELIX 8 AA8 GLY A 303 SER A 308 5 6
HELIX 9 AA9 TYR A 324 CYS A 334 1 11
HELIX 10 AB1 VAL A 350 ALA A 360 5 11
HELIX 11 AB2 GLY A 362 LYS A 370 1 9
HELIX 12 AB3 ASP A 376 GLY A 397 1 22
HELIX 13 AB4 ASP A 401 ASP A 406 5 6
HELIX 14 AB5 CYS A 407 GLY A 411 5 5
HELIX 15 AB6 ASN B 100 GLY B 112 1 13
HELIX 16 AB7 HIS B 114 GLY B 126 1 13
HELIX 17 AB8 PHE B 156 LEU B 159 5 4
HELIX 18 AB9 TYR B 160 HIS B 170 1 11
HELIX 19 AC1 ASP B 192 ILE B 198 1 7
HELIX 20 AC2 GLU B 213 HIS B 241 1 29
HELIX 21 AC3 ASP B 254 LYS B 259 5 6
HELIX 22 AC4 SER B 273 ASP B 286 1 14
HELIX 23 AC5 VAL B 306 ILE B 310 5 5
HELIX 24 AC6 TYR B 324 CYS B 334 1 11
HELIX 25 AC7 VAL B 350 PHE B 359 5 10
HELIX 26 AC8 GLY B 362 LEU B 369 1 8
HELIX 27 AC9 ASP B 376 GLY B 397 1 22
HELIX 28 AD1 ASP B 401 ASP B 406 5 6
SHEET 1 AA111 ASP A 94 LEU A 96 0
SHEET 2 AA111 THR A 129 TRP A 134 -1 O THR A 130 N THR A 95
SHEET 3 AA111 VAL A 65 PHE A 72 1 N VAL A 65 O ASN A 133
SHEET 4 AA111 THR A 79 PRO A 86 -1 O TYR A 85 N GLY A 66
SHEET 5 AA111 ILE A 173 VAL A 177 -1 O ALA A 176 N ARG A 82
SHEET 6 AA111 TYR A 144 SER A 150 1 N PHE A 149 O ALA A 175
SHEET 7 AA111 ILE A 262 HIS A 272 1 O ILE A 270 N VAL A 148
SHEET 8 AA111 CYS A 291 LEU A 295 1 O ILE A 293 N VAL A 269
SHEET 9 AA111 LEU A 314 SER A 319 1 O PHE A 315 N GLY A 292
SHEET 10 AA111 ARG A 341 ILE A 346 1 O ILE A 346 N ASN A 318
SHEET 11 AA111 LEU A 416 PRO A 418 -1 O ILE A 417 N THR A 345
SHEET 1 AA2 2 ALA A 186 TYR A 189 0
SHEET 2 AA2 2 SER A 202 TYR A 205 -1 O SER A 202 N TYR A 189
SHEET 1 AA310 ASN B 133 TRP B 134 0
SHEET 2 AA310 VAL B 65 PHE B 72 1 N VAL B 65 O ASN B 133
SHEET 3 AA310 THR B 79 PRO B 86 -1 O THR B 79 N PHE B 72
SHEET 4 AA310 ILE B 173 VAL B 177 -1 O ALA B 176 N ARG B 82
SHEET 5 AA310 TYR B 144 SER B 150 1 N VAL B 147 O ALA B 175
SHEET 6 AA310 ILE B 262 HIS B 272 1 O LYS B 266 N LEU B 146
SHEET 7 AA310 GLY B 292 LEU B 295 1 O LEU B 295 N GLY B 271
SHEET 8 AA310 LEU B 314 SER B 319 1 O PHE B 315 N ALA B 294
SHEET 9 AA310 ARG B 341 ILE B 346 1 O LYS B 342 N PHE B 316
SHEET 10 AA310 LEU B 416 PRO B 418 -1 O ILE B 417 N THR B 345
SHEET 1 AA4 2 ALA B 186 TYR B 189 0
SHEET 2 AA4 2 SER B 202 TYR B 205 -1 O LEU B 204 N THR B 187
LINK OG SER A 273 C1 BWO A 501 1555 1555 1.51
LINK OG SER B 273 C1 BWO B 501 1555 1555 1.48
CISPEP 1 PHE A 72 ASP A 73 0 -7.43
CISPEP 2 PHE B 72 ASP B 73 0 -21.35
SITE 1 AC1 16 LEU A 107 PHE A 110 LEU A 121 GLY A 152
SITE 2 AC1 16 LEU A 153 GLY A 154 LEU A 159 SER A 273
SITE 3 AC1 16 PHE A 274 TRP A 298 PHE A 322 HIS A 351
SITE 4 AC1 16 GLN A 352 PHE A 357 LEU A 369 LEU A 371
SITE 1 AC2 21 LEU B 107 PHE B 110 LEU B 121 GLY B 152
SITE 2 AC2 21 LEU B 153 GLY B 154 LEU B 159 HIS B 272
SITE 3 AC2 21 PHE B 274 GLY B 275 GLY B 276 ALA B 277
SITE 4 AC2 21 LEU B 295 ASP B 296 ALA B 297 TRP B 298
SITE 5 AC2 21 HIS B 351 GLN B 352 PHE B 357 LEU B 369
SITE 6 AC2 21 LEU B 371
CRYST1 112.687 77.857 94.698 90.00 115.32 90.00 C 1 2 1 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 0.008874 0.000000 0.004199 0.00000
SCALE2 0.000000 0.012844 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011682 0.00000
TER 2829 ILE A 422
TER 5659 ILE B 422
MASTER 382 0 2 28 25 0 10 6 5749 2 88 58
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