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 2 22-NOV-23 5YEA 1 REMARK 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