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HEADER HYDROLASE/HYDROLASE INHIBITOR 15-SEP-17 5YEA
TITLE THE CRYSTAL STRUCTURE OF LP-PLA2 IN COMPLEX WITH A NOVEL INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 47-429;
COMPND 5 SYNONYM: LP-PLA2,PAF ACETYLHYDROLASE,1-ALKYL-2-
COMPND 6 ACETYLGLYCEROPHOSPHOCHOLINE ESTERASE,2-ACETYL-1-
COMPND 7 ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE,GROUP-VIIA PHOSPHOLIPASE A2,
COMPND 8 GVIIA-PLA2,LDL-ASSOCIATED PHOSPHOLIPASE A2,LDL-PLA(2),PAF 2-
COMPND 9 ACYLHYDROLASE;
COMPND 10 EC: 3.1.1.47;
COMPND 11 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;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HYDROLASE INHIBITOR, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Q.F.LIU,Y.C.XU
REVDAT 1 25-JUL-18 5YEA 0
JRNL AUTH Q.LIU,F.HUANG,X.YUAN,K.WANG,Y.ZOU,J.SHEN,Y.XU
JRNL TITL STRUCTURE-GUIDED DISCOVERY OF NOVEL, POTENT, AND ORALLY
JRNL TITL 2 BIOAVAILABLE INHIBITORS OF LIPOPROTEIN-ASSOCIATED
JRNL TITL 3 PHOSPHOLIPASE A2.
JRNL REF J. MED. CHEM. V. 60 10231 2017
JRNL REFN ISSN 1520-4804
JRNL PMID 29193967
JRNL DOI 10.1021/ACS.JMEDCHEM.7B01530
REMARK 2
REMARK 2 RESOLUTION. 1.81 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.70
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8
REMARK 3 NUMBER OF REFLECTIONS : 72308
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.211
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930
REMARK 3 FREE R VALUE TEST SET COUNT : 3564
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 37.7037 - 5.2723 1.00 3011 163 0.1794 0.2187
REMARK 3 2 5.2723 - 4.1866 1.00 2958 151 0.1544 0.1792
REMARK 3 3 4.1866 - 3.6579 1.00 2956 152 0.1526 0.1936
REMARK 3 4 3.6579 - 3.3236 1.00 2940 142 0.1638 0.1699
REMARK 3 5 3.3236 - 3.0855 0.99 2911 153 0.1827 0.2133
REMARK 3 6 3.0855 - 2.9037 0.99 2885 166 0.1811 0.2248
REMARK 3 7 2.9037 - 2.7583 0.98 2857 156 0.1852 0.2278
REMARK 3 8 2.7583 - 2.6383 0.98 2869 147 0.1807 0.2246
REMARK 3 9 2.6383 - 2.5367 0.97 2820 160 0.1834 0.2119
REMARK 3 10 2.5367 - 2.4492 0.97 2865 143 0.1821 0.2009
REMARK 3 11 2.4492 - 2.3726 0.96 2786 140 0.1759 0.2288
REMARK 3 12 2.3726 - 2.3048 0.96 2820 142 0.1808 0.2105
REMARK 3 13 2.3048 - 2.2442 0.97 2830 148 0.1768 0.1981
REMARK 3 14 2.2442 - 2.1894 0.97 2845 141 0.1711 0.2055
REMARK 3 15 2.1894 - 2.1397 0.97 2831 141 0.1722 0.1938
REMARK 3 16 2.1397 - 2.0941 0.98 2852 135 0.1742 0.2343
REMARK 3 17 2.0941 - 2.0522 0.97 2850 144 0.1808 0.2160
REMARK 3 18 2.0522 - 2.0135 0.96 2816 154 0.1900 0.2112
REMARK 3 19 2.0135 - 1.9776 0.96 2783 132 0.1903 0.2101
REMARK 3 20 1.9776 - 1.9440 0.95 2808 139 0.1949 0.2642
REMARK 3 21 1.9440 - 1.9127 0.93 2700 143 0.2024 0.2501
REMARK 3 22 1.9127 - 1.8832 0.90 2588 151 0.2172 0.2627
REMARK 3 23 1.8832 - 1.8556 0.82 2406 126 0.2246 0.2764
REMARK 3 24 1.8556 - 1.8294 0.76 2171 118 0.2395 0.3012
REMARK 3 25 1.8294 - 1.8047 0.53 1586 77 0.2660 0.2849
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.660
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 19.55
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.02
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.009 5979
REMARK 3 ANGLE : 0.952 8125
REMARK 3 CHIRALITY : 0.055 878
REMARK 3 PLANARITY : 0.006 1043
REMARK 3 DIHEDRAL : 7.383 3519
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5YEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-SEP-17.
REMARK 100 THE DEPOSITION ID IS D_1300005136.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-JUL-17
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 : BL17U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75281
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
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 (%) : 98.3
REMARK 200 DATA REDUNDANCY : 6.800
REMARK 200 R MERGE (I) : 0.16300
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 5.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 6.70
REMARK 200 R MERGE FOR SHELL (I) : 1.96100
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: NULL
REMARK 200 STARTING MODEL: 5I8P
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.23
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MOPS PH 6.6, 0.4M LI2SO4, 27%
REMARK 280 (W/V) (NH4)2SO4, 1M NA-AC, 1.4% 1,4-BUTANEDIOL, VAPOR DIFFUSION,
REMARK 280 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 57.89550
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.70400
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.89550
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.70400
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14330 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL
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 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 42
REMARK 465 PRO A 43
REMARK 465 LEU A 44
REMARK 465 GLY A 45
REMARK 465 SER A 46
REMARK 465 ALA A 47
REMARK 465 ALA A 48
REMARK 465 ALA A 49
REMARK 465 SER A 50
REMARK 465 PHE A 51
REMARK 465 GLY A 52
REMARK 465 THR A 425
REMARK 465 ASN A 426
REMARK 465 GLN A 427
REMARK 465 HIS A 428
REMARK 465 ILE A 429
REMARK 465 GLY B 42
REMARK 465 PRO B 43
REMARK 465 LEU B 44
REMARK 465 GLY B 45
REMARK 465 SER B 46
REMARK 465 ALA B 47
REMARK 465 ALA B 48
REMARK 465 ALA B 49
REMARK 465 SER B 50
REMARK 465 PHE B 51
REMARK 465 GLY B 52
REMARK 465 GLN B 53
REMARK 465 THR B 54
REMARK 465 ASN B 426
REMARK 465 GLN B 427
REMARK 465 HIS B 428
REMARK 465 ILE B 429
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLN A 53 CG CD OE1 NE2
REMARK 470 LYS A 55 CG CD CE NZ
REMARK 470 GLN A 88 CG CD OE1 NE2
REMARK 470 ASP A 89 CG OD1 OD2
REMARK 470 ASP A 91 CG OD1 OD2
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 LEU A 123 CG CD1 CD2
REMARK 470 LYS A 143 CE NZ
REMARK 470 GLN A 193 CD OE1 NE2
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 GLU A 220 OE1 OE2
REMARK 470 LYS A 227 CD CE NZ
REMARK 470 LYS A 246 CD CE NZ
REMARK 470 LYS A 252 CG CD CE NZ
REMARK 470 GLU A 256 CG CD OE1 OE2
REMARK 470 ASP A 304 CG OD1 OD2
REMARK 470 LYS A 363 CG CD CE NZ
REMARK 470 MET A 368 CG SD CE
REMARK 470 LYS A 370 CG CD CE NZ
REMARK 470 GLU A 414 CG CD OE1 OE2
REMARK 470 LYS B 55 CG CD CE NZ
REMARK 470 ARG B 58 CD NE CZ NH1 NH2
REMARK 470 GLN B 88 CG CD OE1 NE2
REMARK 470 ASP B 89 CG OD1 OD2
REMARK 470 ASN B 90 CG OD1 ND2
REMARK 470 ASP B 91 CG OD1 OD2
REMARK 470 ARG B 92 CG CD NE CZ NH1 NH2
REMARK 470 LEU B 93 CG CD1 CD2
REMARK 470 LYS B 109 CG CD CE NZ
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 ASN B 133 OD1 ND2
REMARK 470 GLU B 142 CG CD OE1 OE2
REMARK 470 LYS B 143 CE NZ
REMARK 470 GLN B 193 CD OE1 NE2
REMARK 470 GLU B 197 CG CD OE1 OE2
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 LYS B 227 CD CE NZ
REMARK 470 LYS B 246 CD CE NZ
REMARK 470 LYS B 252 CG CD CE NZ
REMARK 470 GLU B 256 CG CD OE1 OE2
REMARK 470 ARG B 290 CZ NH1 NH2
REMARK 470 ASP B 304 CG OD1 OD2
REMARK 470 ARG B 347 CG CD NE CZ NH1 NH2
REMARK 470 LYS B 363 CG CD CE NZ
REMARK 470 MET B 368 CG SD CE
REMARK 470 LYS B 370 CG CD CE NZ
REMARK 470 GLU B 414 CG CD OE1 OE2
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 NH2 ARG A 92 O HOH A 601 1.80
REMARK 500 NH1 ARG A 92 O HOH A 602 2.14
REMARK 500 OG SER A 336 OD1 ASP A 338 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NE ARG A 92 OD2 ASP B 200 3555 1.78
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 ARG A 92 CB ARG A 92 CG 0.276
REMARK 500 ARG A 92 CG ARG A 92 CD 0.222
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 92 CA - CB - CG ANGL. DEV. = 21.0 DEGREES
REMARK 500 ARG A 92 CB - CG - CD ANGL. DEV. = 26.2 DEGREES
REMARK 500 ARG A 92 CD - NE - CZ ANGL. DEV. = 20.0 DEGREES
REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = -7.4 DEGREES
REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = 12.1 DEGREES
REMARK 500 ASP B 200 CB - CG - OD2 ANGL. DEV. = 11.3 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 ASN A 90 54.60 -119.54
REMARK 500 HIS A 114 -166.45 -116.47
REMARK 500 LYS A 252 36.47 -83.17
REMARK 500 LYS A 266 74.79 -115.72
REMARK 500 SER A 273 -114.85 63.54
REMARK 500 HIS A 399 63.69 -108.62
REMARK 500 ASP B 73 -165.30 -78.12
REMARK 500 LEU B 93 72.85 -118.49
REMARK 500 THR B 113 -165.44 -107.12
REMARK 500 HIS B 114 -158.03 -135.53
REMARK 500 LYS B 266 74.45 -115.46
REMARK 500 SER B 273 -118.30 65.98
REMARK 500 HIS B 399 61.02 -107.80
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 SO4 A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8U9 A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8U9 B 502
DBREF 5YEA A 47 429 UNP Q13093 PAFA_HUMAN 47 429
DBREF 5YEA B 47 429 UNP Q13093 PAFA_HUMAN 47 429
SEQADV 5YEA GLY A 42 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA PRO A 43 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA LEU A 44 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA GLY A 45 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA SER A 46 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA GLY B 42 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA PRO B 43 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA LEU B 44 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA GLY B 45 UNP Q13093 EXPRESSION TAG
SEQADV 5YEA SER B 46 UNP Q13093 EXPRESSION TAG
SEQRES 1 A 388 GLY PRO LEU GLY SER ALA ALA ALA SER PHE GLY GLN THR
SEQRES 2 A 388 LYS ILE PRO ARG GLY ASN GLY PRO TYR SER VAL GLY CYS
SEQRES 3 A 388 THR ASP LEU MET PHE ASP HIS THR ASN LYS GLY THR PHE
SEQRES 4 A 388 LEU ARG LEU TYR TYR PRO SER GLN ASP ASN ASP ARG LEU
SEQRES 5 A 388 ASP THR LEU TRP ILE PRO ASN LYS GLU TYR PHE TRP GLY
SEQRES 6 A 388 LEU SER LYS PHE LEU GLY THR HIS TRP LEU MET GLY ASN
SEQRES 7 A 388 ILE LEU ARG LEU LEU PHE GLY SER MET THR THR PRO ALA
SEQRES 8 A 388 ASN TRP ASN SER PRO LEU ARG PRO GLY GLU LYS TYR PRO
SEQRES 9 A 388 LEU VAL VAL PHE SER HIS GLY LEU GLY ALA PHE ARG THR
SEQRES 10 A 388 LEU TYR SER ALA ILE GLY ILE ASP LEU ALA SER HIS GLY
SEQRES 11 A 388 PHE ILE VAL ALA ALA VAL GLU HIS ARG ASP ARG SER ALA
SEQRES 12 A 388 SER ALA THR TYR TYR PHE LYS ASP GLN SER ALA ALA GLU
SEQRES 13 A 388 ILE GLY ASP LYS SER TRP LEU TYR LEU ARG THR LEU LYS
SEQRES 14 A 388 GLN GLU GLU GLU THR HIS ILE ARG ASN GLU GLN VAL ARG
SEQRES 15 A 388 GLN ARG ALA LYS GLU CYS SER GLN ALA LEU SER LEU ILE
SEQRES 16 A 388 LEU ASP ILE ASP HIS GLY LYS PRO VAL LYS ASN ALA LEU
SEQRES 17 A 388 ASP LEU LYS PHE ASP MET GLU GLN LEU LYS ASP SER ILE
SEQRES 18 A 388 ASP ARG GLU LYS ILE ALA VAL ILE GLY HIS SER PHE GLY
SEQRES 19 A 388 GLY ALA THR VAL ILE GLN THR LEU SER GLU ASP GLN ARG
SEQRES 20 A 388 PHE ARG CYS GLY ILE ALA LEU ASP ALA TRP MET PHE PRO
SEQRES 21 A 388 LEU GLY ASP GLU VAL TYR SER ARG ILE PRO GLN PRO LEU
SEQRES 22 A 388 PHE PHE ILE ASN SER GLU TYR PHE GLN TYR PRO ALA ASN
SEQRES 23 A 388 ILE ILE LYS MET LYS LYS CYS TYR SER PRO ASP LYS GLU
SEQRES 24 A 388 ARG LYS MET ILE THR ILE ARG GLY SER VAL HIS GLN ASN
SEQRES 25 A 388 PHE ALA ASP PHE THR PHE ALA THR GLY LYS ILE ILE GLY
SEQRES 26 A 388 HIS MET LEU LYS LEU LYS GLY ASP ILE ASP SER ASN VAL
SEQRES 27 A 388 ALA ILE ASP LEU SER ASN LYS ALA SER LEU ALA PHE LEU
SEQRES 28 A 388 GLN LYS HIS LEU GLY LEU HIS LYS ASP PHE ASP GLN TRP
SEQRES 29 A 388 ASP CYS LEU ILE GLU GLY ASP ASP GLU ASN LEU ILE PRO
SEQRES 30 A 388 GLY THR ASN ILE ASN THR THR ASN GLN HIS ILE
SEQRES 1 B 388 GLY PRO LEU GLY SER ALA ALA ALA SER PHE GLY GLN THR
SEQRES 2 B 388 LYS ILE PRO ARG GLY ASN GLY PRO TYR SER VAL GLY CYS
SEQRES 3 B 388 THR ASP LEU MET PHE ASP HIS THR ASN LYS GLY THR PHE
SEQRES 4 B 388 LEU ARG LEU TYR TYR PRO SER GLN ASP ASN ASP ARG LEU
SEQRES 5 B 388 ASP THR LEU TRP ILE PRO ASN LYS GLU TYR PHE TRP GLY
SEQRES 6 B 388 LEU SER LYS PHE LEU GLY THR HIS TRP LEU MET GLY ASN
SEQRES 7 B 388 ILE LEU ARG LEU LEU PHE GLY SER MET THR THR PRO ALA
SEQRES 8 B 388 ASN TRP ASN SER PRO LEU ARG PRO GLY GLU LYS TYR PRO
SEQRES 9 B 388 LEU VAL VAL PHE SER HIS GLY LEU GLY ALA PHE ARG THR
SEQRES 10 B 388 LEU TYR SER ALA ILE GLY ILE ASP LEU ALA SER HIS GLY
SEQRES 11 B 388 PHE ILE VAL ALA ALA VAL GLU HIS ARG ASP ARG SER ALA
SEQRES 12 B 388 SER ALA THR TYR TYR PHE LYS ASP GLN SER ALA ALA GLU
SEQRES 13 B 388 ILE GLY ASP LYS SER TRP LEU TYR LEU ARG THR LEU LYS
SEQRES 14 B 388 GLN GLU GLU GLU THR HIS ILE ARG ASN GLU GLN VAL ARG
SEQRES 15 B 388 GLN ARG ALA LYS GLU CYS SER GLN ALA LEU SER LEU ILE
SEQRES 16 B 388 LEU ASP ILE ASP HIS GLY LYS PRO VAL LYS ASN ALA LEU
SEQRES 17 B 388 ASP LEU LYS PHE ASP MET GLU GLN LEU LYS ASP SER ILE
SEQRES 18 B 388 ASP ARG GLU LYS ILE ALA VAL ILE GLY HIS SER PHE GLY
SEQRES 19 B 388 GLY ALA THR VAL ILE GLN THR LEU SER GLU ASP GLN ARG
SEQRES 20 B 388 PHE ARG CYS GLY ILE ALA LEU ASP ALA TRP MET PHE PRO
SEQRES 21 B 388 LEU GLY ASP GLU VAL TYR SER ARG ILE PRO GLN PRO LEU
SEQRES 22 B 388 PHE PHE ILE ASN SER GLU TYR PHE GLN TYR PRO ALA ASN
SEQRES 23 B 388 ILE ILE LYS MET LYS LYS CYS TYR SER PRO ASP LYS GLU
SEQRES 24 B 388 ARG LYS MET ILE THR ILE ARG GLY SER VAL HIS GLN ASN
SEQRES 25 B 388 PHE ALA ASP PHE THR PHE ALA THR GLY LYS ILE ILE GLY
SEQRES 26 B 388 HIS MET LEU LYS LEU LYS GLY ASP ILE ASP SER ASN VAL
SEQRES 27 B 388 ALA ILE ASP LEU SER ASN LYS ALA SER LEU ALA PHE LEU
SEQRES 28 B 388 GLN LYS HIS LEU GLY LEU HIS LYS ASP PHE ASP GLN TRP
SEQRES 29 B 388 ASP CYS LEU ILE GLU GLY ASP ASP GLU ASN LEU ILE PRO
SEQRES 30 B 388 GLY THR ASN ILE ASN THR THR ASN GLN HIS ILE
HET SO4 A 501 5
HET SO4 A 502 5
HET 8U9 A 503 33
HET SO4 B 501 5
HET 8U9 B 502 33
HETNAM SO4 SULFATE ION
HETNAM 8U9 4-[[4-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENOXY]-3-CYANO-
HETNAM 2 8U9 PHENYL]SULFAMOYL]BENZOIC ACID
FORMUL 3 SO4 3(O4 S 2-)
FORMUL 5 8U9 2(C21 H12 CL F3 N2 O5 S)
FORMUL 8 HOH *395(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 ARG A 309 5 7
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 HIS B 170 1 11
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 GLY B 303 TYR B 307 5 5
HELIX 25 AC7 TYR B 324 CYS B 334 1 11
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 ILE A 344 N ASN A 318
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 VAL B 65 PHE B 72 1 N VAL B 65 O ASN B 133
SHEET 3 AA410 THR B 79 PRO B 86 -1 O LEU B 83 N THR B 68
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 ASP B 263 N TYR B 144
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 ILE B 344 N ASN B 318
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
CISPEP 1 PHE A 72 ASP A 73 0 -4.74
CISPEP 2 PHE B 72 ASP B 73 0 -2.93
SITE 1 AC1 7 ASP A 89 ASN A 90 HOH A 603 HOH A 648
SITE 2 AC1 7 ASN B 100 LYS B 101 ARG B 122
SITE 1 AC2 9 LYS A 101 GLY A 199 LYS A 201 HOH A 607
SITE 2 AC2 9 HOH A 614 HOH A 630 HOH A 721 ARG B 182
SITE 3 AC2 9 ARG B 207
SITE 1 AC3 14 LEU A 107 PHE A 110 LEU A 111 LEU A 121
SITE 2 AC3 14 GLY A 152 LEU A 153 GLY A 154 ALA A 155
SITE 3 AC3 14 HIS A 272 SER A 273 GLN A 352 ALA A 355
SITE 4 AC3 14 ASP A 356 PHE A 357
SITE 1 AC4 9 HIS A 241 ARG A 264 HOH A 628 SER B 308
SITE 2 AC4 9 ARG B 309 ILE B 310 PRO B 311 LYS B 339
SITE 3 AC4 9 HOH B 603
SITE 1 AC5 15 LEU B 107 PHE B 110 LEU B 111 LEU B 121
SITE 2 AC5 15 GLY B 152 LEU B 153 GLY B 154 HIS B 272
SITE 3 AC5 15 SER B 273 GLN B 352 ALA B 355 ASP B 356
SITE 4 AC5 15 PHE B 357 LEU B 371 HOH B 606
CRYST1 115.791 83.408 96.889 90.00 114.57 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 0.008636 0.000000 0.003948 0.00000
SCALE2 0.000000 0.011989 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011348 0.00000
TER 2895 THR A 424
TER 5756 THR B 425
MASTER 459 0 5 30 28 0 16 6 6230 2 81 60
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