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HEADER HYDROLASE 20-FEB-20 6M06
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 PHOSPHOLIPASE,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.C.HU,Y.C.XU
REVDAT 2 13-JAN-21 6M06 1 COMPND HETNAM FORMUL
REVDAT 1 30-DEC-20 6M06 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. 2.10 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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.79
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 45526
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) : 0.188
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.220
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 2352
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2883
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.03
REMARK 3 BIN R VALUE (WORKING SET) : 0.2160
REMARK 3 BIN FREE R VALUE SET COUNT : 167
REMARK 3 BIN FREE R VALUE : 0.2570
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5785
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 26
REMARK 3 SOLVENT ATOMS : 172
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.99
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.26000
REMARK 3 B22 (A**2) : -0.32000
REMARK 3 B33 (A**2) : 0.32000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.13000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.211
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.171
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.874
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5955 ; 0.009 ; 0.013
REMARK 3 BOND LENGTHS OTHERS (A): 5318 ; 0.003 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8082 ; 1.471 ; 1.642
REMARK 3 BOND ANGLES OTHERS (DEGREES): 12298 ; 1.591 ; 1.579
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 740 ; 6.970 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 310 ;35.335 ;22.323
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 944 ;15.920 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.257 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 781 ; 0.075 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6778 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1314 ; 0.008 ; 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 6M06 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_1300015780.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-MAY-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL19U1
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 : 48714
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
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 (%) : 99.9
REMARK 200 DATA REDUNDANCY : 6.200
REMARK 200 R MERGE (I) : 0.18800
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 5.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 5.10
REMARK 200 R MERGE FOR SHELL (I) : 0.73900
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 (%): 50.77
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50
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 58.00700
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.61000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.00700
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.61000
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 ARG A 92 NE CZ NH1 NH2
REMARK 470 LYS A 101 CG CD CE NZ
REMARK 470 LYS A 109 CG CD CE NZ
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 LYS A 210 CG CD CE NZ
REMARK 470 GLN A 211 CG CD OE1 NE2
REMARK 470 GLU A 212 OE1 OE2
REMARK 470 LYS A 227 CG CD CE NZ
REMARK 470 LYS A 243 CG CD 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 CD CE NZ
REMARK 470 ASP A 304 CG OD1 OD2
REMARK 470 LYS A 333 CE NZ
REMARK 470 LYS A 363 CG CD CE NZ
REMARK 470 LYS A 370 CG CD CE NZ
REMARK 470 GLU A 414 CG CD OE1 OE2
REMARK 470 ILE A 417 CD1
REMARK 470 ASN A 423 CG OD1 ND2
REMARK 470 THR A 424 OG1 CG2
REMARK 470 THR B 54 OG1 CG2
REMARK 470 LYS B 55 CG CD CE NZ
REMARK 470 ASP B 89 CG OD1 OD2
REMARK 470 ASP B 91 CG OD1 OD2
REMARK 470 ARG B 92 NE CZ NH1 NH2
REMARK 470 LYS B 109 CG CD CE NZ
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 LYS B 143 CE NZ
REMARK 470 LYS B 210 CG CD CE NZ
REMARK 470 GLN B 211 CG CD OE1 NE2
REMARK 470 GLU B 212 OE1 OE2
REMARK 470 LYS B 227 CG CD CE NZ
REMARK 470 LYS B 246 CG CD CE NZ
REMARK 470 LYS B 252 CG CD CE NZ
REMARK 470 LYS B 259 CD CE NZ
REMARK 470 ASP B 304 CG OD1 OD2
REMARK 470 LYS B 363 CG CD CE NZ
REMARK 470 LYS B 370 CG CD CE NZ
REMARK 470 GLU B 414 CG CD OE1 OE2
REMARK 470 ILE B 417 CD1
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 NH1 ARG B 347 CG1 ILE B 417 2.03
REMARK 500 NE2 HIS A 216 OE1 GLU A 220 2.05
REMARK 500 CE1 HIS A 216 OE1 GLU A 220 2.07
REMARK 500 OG SER B 273 O3 BWF B 501 2.14
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES
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 HIS A 114 -132.62 -124.26
REMARK 500 LYS A 266 76.77 -115.71
REMARK 500 SER A 273 -112.88 62.25
REMARK 500 HIS A 399 54.03 -104.04
REMARK 500 LYS A 400 -162.83 -121.31
REMARK 500 ASP B 73 -164.09 -77.00
REMARK 500 LEU B 93 61.10 -111.13
REMARK 500 THR B 113 -162.25 -107.73
REMARK 500 HIS B 114 -154.09 -117.47
REMARK 500 PHE B 156 -178.55 -173.78
REMARK 500 LYS B 266 74.80 -117.16
REMARK 500 SER B 273 -117.93 64.51
REMARK 500 HIS B 399 64.29 -107.56
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 BWF A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BWF B 501 and SER B
REMARK 800 273
DBREF 6M06 A 54 424 UNP Q13093 PAFA_HUMAN 54 424
DBREF 6M06 B 54 424 UNP Q13093 PAFA_HUMAN 54 424
SEQRES 1 A 371 THR LYS ILE PRO ARG GLY ASN GLY PRO TYR SER VAL GLY
SEQRES 2 A 371 CYS THR ASP LEU MET PHE ASP HIS THR ASN LYS GLY THR
SEQRES 3 A 371 PHE LEU ARG LEU TYR TYR PRO SER GLN ASP ASN ASP ARG
SEQRES 4 A 371 LEU ASP THR LEU TRP ILE PRO ASN LYS GLU TYR PHE TRP
SEQRES 5 A 371 GLY LEU SER LYS PHE LEU GLY THR HIS TRP LEU MET GLY
SEQRES 6 A 371 ASN ILE LEU ARG LEU LEU PHE GLY SER MET THR THR PRO
SEQRES 7 A 371 ALA ASN TRP ASN SER PRO LEU ARG PRO GLY GLU LYS TYR
SEQRES 8 A 371 PRO LEU VAL VAL PHE SER HIS GLY LEU GLY ALA PHE ARG
SEQRES 9 A 371 THR LEU TYR SER ALA ILE GLY ILE ASP LEU ALA SER HIS
SEQRES 10 A 371 GLY PHE ILE VAL ALA ALA VAL GLU HIS ARG ASP ARG SER
SEQRES 11 A 371 ALA SER ALA THR TYR TYR PHE LYS ASP GLN SER ALA ALA
SEQRES 12 A 371 GLU ILE GLY ASP LYS SER TRP LEU TYR LEU ARG THR LEU
SEQRES 13 A 371 LYS GLN GLU GLU GLU THR HIS ILE ARG ASN GLU GLN VAL
SEQRES 14 A 371 ARG GLN ARG ALA LYS GLU CYS SER GLN ALA LEU SER LEU
SEQRES 15 A 371 ILE LEU ASP ILE ASP HIS GLY LYS PRO VAL LYS ASN ALA
SEQRES 16 A 371 LEU ASP LEU LYS PHE ASP MET GLU GLN LEU LYS ASP SER
SEQRES 17 A 371 ILE ASP ARG GLU LYS ILE ALA VAL ILE GLY HIS SER PHE
SEQRES 18 A 371 GLY GLY ALA THR VAL ILE GLN THR LEU SER GLU ASP GLN
SEQRES 19 A 371 ARG PHE ARG CYS GLY ILE ALA LEU ASP ALA TRP MET PHE
SEQRES 20 A 371 PRO LEU GLY ASP GLU VAL TYR SER ARG ILE PRO GLN PRO
SEQRES 21 A 371 LEU PHE PHE ILE ASN SER GLU TYR PHE GLN TYR PRO ALA
SEQRES 22 A 371 ASN ILE ILE LYS MET LYS LYS CYS TYR SER PRO ASP LYS
SEQRES 23 A 371 GLU ARG LYS MET ILE THR ILE ARG GLY SER VAL HIS GLN
SEQRES 24 A 371 ASN PHE ALA ASP PHE THR PHE ALA THR GLY LYS ILE ILE
SEQRES 25 A 371 GLY HIS MET LEU LYS LEU LYS GLY ASP ILE ASP SER ASN
SEQRES 26 A 371 VAL ALA ILE ASP LEU SER ASN LYS ALA SER LEU ALA PHE
SEQRES 27 A 371 LEU GLN LYS HIS LEU GLY LEU HIS LYS ASP PHE ASP GLN
SEQRES 28 A 371 TRP ASP CYS LEU ILE GLU GLY ASP ASP GLU ASN LEU ILE
SEQRES 29 A 371 PRO GLY THR ASN ILE ASN THR
SEQRES 1 B 371 THR LYS ILE PRO ARG GLY ASN GLY PRO TYR SER VAL GLY
SEQRES 2 B 371 CYS THR ASP LEU MET PHE ASP HIS THR ASN LYS GLY THR
SEQRES 3 B 371 PHE LEU ARG LEU TYR TYR PRO SER GLN ASP ASN ASP ARG
SEQRES 4 B 371 LEU ASP THR LEU TRP ILE PRO ASN LYS GLU TYR PHE TRP
SEQRES 5 B 371 GLY LEU SER LYS PHE LEU GLY THR HIS TRP LEU MET GLY
SEQRES 6 B 371 ASN ILE LEU ARG LEU LEU PHE GLY SER MET THR THR PRO
SEQRES 7 B 371 ALA ASN TRP ASN SER PRO LEU ARG PRO GLY GLU LYS TYR
SEQRES 8 B 371 PRO LEU VAL VAL PHE SER HIS GLY LEU GLY ALA PHE ARG
SEQRES 9 B 371 THR LEU TYR SER ALA ILE GLY ILE ASP LEU ALA SER HIS
SEQRES 10 B 371 GLY PHE ILE VAL ALA ALA VAL GLU HIS ARG ASP ARG SER
SEQRES 11 B 371 ALA SER ALA THR TYR TYR PHE LYS ASP GLN SER ALA ALA
SEQRES 12 B 371 GLU ILE GLY ASP LYS SER TRP LEU TYR LEU ARG THR LEU
SEQRES 13 B 371 LYS GLN GLU GLU GLU THR HIS ILE ARG ASN GLU GLN VAL
SEQRES 14 B 371 ARG GLN ARG ALA LYS GLU CYS SER GLN ALA LEU SER LEU
SEQRES 15 B 371 ILE LEU ASP ILE ASP HIS GLY LYS PRO VAL LYS ASN ALA
SEQRES 16 B 371 LEU ASP LEU LYS PHE ASP MET GLU GLN LEU LYS ASP SER
SEQRES 17 B 371 ILE ASP ARG GLU LYS ILE ALA VAL ILE GLY HIS SER PHE
SEQRES 18 B 371 GLY GLY ALA THR VAL ILE GLN THR LEU SER GLU ASP GLN
SEQRES 19 B 371 ARG PHE ARG CYS GLY ILE ALA LEU ASP ALA TRP MET PHE
SEQRES 20 B 371 PRO LEU GLY ASP GLU VAL TYR SER ARG ILE PRO GLN PRO
SEQRES 21 B 371 LEU PHE PHE ILE ASN SER GLU TYR PHE GLN TYR PRO ALA
SEQRES 22 B 371 ASN ILE ILE LYS MET LYS LYS CYS TYR SER PRO ASP LYS
SEQRES 23 B 371 GLU ARG LYS MET ILE THR ILE ARG GLY SER VAL HIS GLN
SEQRES 24 B 371 ASN PHE ALA ASP PHE THR PHE ALA THR GLY LYS ILE ILE
SEQRES 25 B 371 GLY HIS MET LEU LYS LEU LYS GLY ASP ILE ASP SER ASN
SEQRES 26 B 371 VAL ALA ILE ASP LEU SER ASN LYS ALA SER LEU ALA PHE
SEQRES 27 B 371 LEU GLN LYS HIS LEU GLY LEU HIS LYS ASP PHE ASP GLN
SEQRES 28 B 371 TRP ASP CYS LEU ILE GLU GLY ASP ASP GLU ASN LEU ILE
SEQRES 29 B 371 PRO GLY THR ASN ILE ASN THR
HET BWF A 501 13
HET BWF B 501 13
HETNAM BWF (2S)-2-[(Z)-1,3-BIS(OXIDANYL)-3-OXIDANYLIDENE-PROP-1-
HETNAM 2 BWF ENYL]PYRROLIDINE-1-CARBOXYLIC ACID
FORMUL 3 BWF 2(C8 H11 N O5)
FORMUL 5 HOH *172(H2 O)
HELIX 1 AA1 ASN A 100 LEU A 111 1 12
HELIX 2 AA2 HIS A 114 GLY A 126 1 13
HELIX 3 AA3 TYR A 160 HIS A 170 1 11
HELIX 4 AA4 ASP A 192 GLY A 199 1 8
HELIX 5 AA5 LYS A 210 GLU A 212 5 3
HELIX 6 AA6 GLU A 213 HIS A 241 1 29
HELIX 7 AA7 ASP A 254 LYS A 259 5 6
HELIX 8 AA8 SER A 273 ASP A 286 1 14
HELIX 9 AA9 GLY A 303 TYR A 307 5 5
HELIX 10 AB1 TYR A 324 LYS A 333 1 10
HELIX 11 AB2 VAL A 350 ALA A 360 5 11
HELIX 12 AB3 GLY A 362 LEU A 369 1 8
HELIX 13 AB4 ASP A 376 GLY A 397 1 22
HELIX 14 AB5 ASP A 401 GLN A 404 5 4
HELIX 15 AB6 TRP A 405 GLU A 410 1 6
HELIX 16 AB7 ASN B 100 GLY B 112 1 13
HELIX 17 AB8 HIS B 114 GLY B 126 1 13
HELIX 18 AB9 TYR B 160 SER B 169 1 10
HELIX 19 AC1 ASP B 192 ILE B 198 1 7
HELIX 20 AC2 LYS B 210 GLU B 212 5 3
HELIX 21 AC3 GLU B 213 HIS B 241 1 29
HELIX 22 AC4 ASP B 254 LYS B 259 5 6
HELIX 23 AC5 SER B 273 ASP B 286 1 14
HELIX 24 AC6 GLU B 305 ARG B 309 5 5
HELIX 25 AC7 TYR B 324 LYS B 333 1 10
HELIX 26 AC8 VAL B 350 ALA B 360 5 11
HELIX 27 AC9 GLY B 362 LEU B 369 1 8
HELIX 28 AD1 ASP B 376 GLY B 397 1 22
HELIX 29 AD2 ASP B 401 GLN B 404 5 4
HELIX 30 AD3 TRP B 405 GLU B 410 1 6
SHEET 1 AA110 ASN A 133 TRP A 134 0
SHEET 2 AA110 VAL A 65 PHE A 72 1 N VAL A 65 O ASN A 133
SHEET 3 AA110 THR A 79 PRO A 86 -1 O TYR A 85 N GLY A 66
SHEET 4 AA110 ILE A 173 VAL A 177 -1 O VAL A 174 N TYR A 84
SHEET 5 AA110 TYR A 144 SER A 150 1 N VAL A 147 O ALA A 175
SHEET 6 AA110 ILE A 262 HIS A 272 1 O ILE A 270 N VAL A 148
SHEET 7 AA110 CYS A 291 LEU A 295 1 O LEU A 295 N GLY A 271
SHEET 8 AA110 LEU A 314 SER A 319 1 O PHE A 315 N ALA A 294
SHEET 9 AA110 ARG A 341 ILE A 346 1 O LYS A 342 N PHE A 316
SHEET 10 AA110 LEU A 416 PRO A 418 -1 O ILE A 417 N THR A 345
SHEET 1 AA2 2 THR A 95 LEU A 96 0
SHEET 2 AA2 2 THR A 129 THR A 130 -1 O THR A 130 N THR A 95
SHEET 1 AA3 2 ALA A 186 TYR A 189 0
SHEET 2 AA3 2 SER A 202 TYR A 205 -1 O LEU A 204 N THR A 187
SHEET 1 AA410 ASN B 133 TRP B 134 0
SHEET 2 AA410 SER B 64 PHE B 72 1 N VAL B 65 O ASN B 133
SHEET 3 AA410 THR B 79 SER B 87 -1 O TYR B 85 N GLY B 66
SHEET 4 AA410 ILE B 173 VAL B 177 -1 O VAL B 174 N TYR B 84
SHEET 5 AA410 TYR B 144 SER B 150 1 N VAL B 147 O ALA B 175
SHEET 6 AA410 ILE B 262 HIS B 272 1 O ALA B 268 N LEU B 146
SHEET 7 AA410 CYS B 291 LEU B 295 1 O LEU B 295 N GLY B 271
SHEET 8 AA410 LEU B 314 SER B 319 1 O PHE B 315 N ALA B 294
SHEET 9 AA410 ARG B 341 ILE B 346 1 O LYS B 342 N PHE B 316
SHEET 10 AA410 LEU B 416 PRO B 418 -1 O ILE B 417 N THR B 345
SHEET 1 AA5 2 THR B 95 LEU B 96 0
SHEET 2 AA5 2 THR B 129 THR B 130 -1 O THR B 130 N THR B 95
SHEET 1 AA6 2 ALA B 186 TYR B 189 0
SHEET 2 AA6 2 SER B 202 TYR B 205 -1 O SER B 202 N TYR B 189
LINK OG SER A 273 C1 BWF A 501 1555 1555 1.38
LINK OG SER B 273 C1 BWF B 501 1555 1555 1.37
CISPEP 1 PHE A 72 ASP A 73 0 -4.22
CISPEP 2 PHE B 72 ASP B 73 0 -6.81
SITE 1 AC1 6 LEU A 153 SER A 273 PHE A 274 PHE A 322
SITE 2 AC1 6 HIS A 351 GLN A 352
SITE 1 AC2 12 PHE B 110 LEU B 153 HIS B 272 PHE B 274
SITE 2 AC2 12 GLY B 275 GLY B 276 ALA B 277 LEU B 295
SITE 3 AC2 12 ASP B 296 TRP B 298 PHE B 322 HIS B 351
CRYST1 116.014 83.220 96.581 90.00 115.04 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 0.008620 0.000000 0.004027 0.00000
SCALE2 0.000000 0.012016 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011428 0.00000
TER 2888 THR A 424
TER 5787 THR B 424
MASTER 369 0 2 30 28 0 5 6 5983 2 28 58
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