PDB Short entry for 3D59 HEADER HYDROLASE 16-MAY-08 3D59 TITLE CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR TITLE 2 ACETYLHYDROLASE 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: PAF ACETYLHYDROLASE, PAF 2-ACYLHYDROLASE, LDL-ASSOCIATED COMPND 6 PHOSPHOLIPASE A2, LDL-PLA(2), 2-ACETYL-1-ALKYLGLYCEROPHOSPHOCHOLINE COMPND 7 ESTERASE, 1-ALKYL-2-ACETYLGLYCEROPHOSPHOCHOLINE ESTERASE; 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; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE, SECRETED PROTEIN, KEYWDS 2 ALPHA/BETA-HYDROLASE-FOLD, LDL-BOUND; LIPOPROTEIN ASSOCIATED KEYWDS 3 PHOSPHOLIPASE A2, LP-PLA2, GROUP VIIA PLA2, GLYCOPROTEIN, HYDROLASE, KEYWDS 4 LIPID DEGRADATION, POLYMORPHISM, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR U.SAMANTA,B.J.BAHNSON REVDAT 5 21-FEB-24 3D59 1 REMARK REVDAT 4 25-OCT-17 3D59 1 REMARK REVDAT 3 24-FEB-09 3D59 1 VERSN REVDAT 2 25-NOV-08 3D59 1 JRNL REVDAT 1 09-SEP-08 3D59 0 JRNL AUTH U.SAMANTA,B.J.BAHNSON JRNL TITL CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET-ACTIVATING FACTOR JRNL TITL 2 ACETYLHYDROLASE: STRUCTURAL IMPLICATION TO LIPOPROTEIN JRNL TITL 3 BINDING AND CATALYSIS. JRNL REF J.BIOL.CHEM. V. 283 31617 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18784071 JRNL DOI 10.1074/JBC.M804750200 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.142 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.131 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 6384 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.131 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 5314 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 100893 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 126 REMARK 3 SOLVENT ATOMS : 511 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 6556.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 38 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 57242 REMARK 3 NUMBER OF RESTRAINTS : 72220 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.053 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.068 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.031 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3D59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-06; 12-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 6.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; APS REMARK 200 BEAMLINE : X29A; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100; 1.006, 1.009 REMARK 200 MONOCHROMATOR : SI(111); SI(111) REMARK 200 OPTICS : ROSENBAUM-ROCK; ROSENBAUM-ROCK REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127359 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, HKL2MAP, RESOLVE, CCP4, SHELXL-97 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.0K, PH 6.60 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 58.09200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.53050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.09200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.53050 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 596 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 652 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 670 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 GLN A 53 REMARK 465 ASN A 426 REMARK 465 GLN A 427 REMARK 465 HIS A 428 REMARK 465 ILE A 429 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 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 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 LYS B 55 CG CD CE NZ 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 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 GLN B 427 CG CD OE1 NE2 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 ASP A 73 -175.77 -68.57 REMARK 500 LYS A 266 75.85 -117.61 REMARK 500 SER A 273 -117.17 64.88 REMARK 500 HIS A 399 57.46 -102.67 REMARK 500 LYS A 400 -167.29 -118.77 REMARK 500 ASP B 73 -169.63 -69.25 REMARK 500 TRP B 115 -36.24 -38.25 REMARK 500 LYS B 266 77.51 -118.13 REMARK 500 SER B 273 -115.78 66.79 REMARK 500 HIS B 399 65.50 -109.68 REMARK 500 ASN B 426 41.17 -106.50 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 ACT A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 16 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 20 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 28 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 29 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 30 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 32 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 33 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 35 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 36 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 39 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 31 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 34 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 37 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 38 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D5E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR REMARK 900 ACETYLHYDROLASE COVALENTLY INHIBITED BY PARAOXON DBREF 3D59 A 47 429 UNP Q13093 PAFA_HUMAN 47 429 DBREF 3D59 B 47 429 UNP Q13093 PAFA_HUMAN 47 429 SEQRES 1 A 383 ALA ALA ALA SER PHE GLY GLN THR LYS ILE PRO ARG GLY SEQRES 2 A 383 ASN GLY PRO TYR SER VAL GLY CYS THR ASP LEU MET PHE SEQRES 3 A 383 ASP HIS THR ASN LYS GLY THR PHE LEU ARG LEU TYR TYR SEQRES 4 A 383 PRO SER GLN ASP ASN ASP ARG LEU ASP THR LEU TRP ILE SEQRES 5 A 383 PRO ASN LYS GLU TYR PHE TRP GLY LEU SER LYS PHE LEU SEQRES 6 A 383 GLY THR HIS TRP LEU MET GLY ASN ILE LEU ARG LEU LEU SEQRES 7 A 383 PHE GLY SER MET THR THR PRO ALA ASN TRP ASN SER PRO SEQRES 8 A 383 LEU ARG PRO GLY GLU LYS TYR PRO LEU VAL VAL PHE SER SEQRES 9 A 383 HIS GLY LEU GLY ALA PHE ARG THR LEU TYR SER ALA ILE SEQRES 10 A 383 GLY ILE ASP LEU ALA SER HIS GLY PHE ILE VAL ALA ALA SEQRES 11 A 383 VAL GLU HIS ARG ASP ARG SER ALA SER ALA THR TYR TYR SEQRES 12 A 383 PHE LYS ASP GLN SER ALA ALA GLU ILE GLY ASP LYS SER SEQRES 13 A 383 TRP LEU TYR LEU ARG THR LEU LYS GLN GLU GLU GLU THR SEQRES 14 A 383 HIS ILE ARG ASN GLU GLN VAL ARG GLN ARG ALA LYS GLU SEQRES 15 A 383 CYS SER GLN ALA LEU SER LEU ILE LEU ASP ILE ASP HIS SEQRES 16 A 383 GLY LYS PRO VAL LYS ASN ALA LEU ASP LEU LYS PHE ASP SEQRES 17 A 383 MET GLU GLN LEU LYS ASP SER ILE ASP ARG GLU LYS ILE SEQRES 18 A 383 ALA VAL ILE GLY HIS SER PHE GLY GLY ALA THR VAL ILE SEQRES 19 A 383 GLN THR LEU SER GLU ASP GLN ARG PHE ARG CYS GLY ILE SEQRES 20 A 383 ALA LEU ASP ALA TRP MET PHE PRO LEU GLY ASP GLU VAL SEQRES 21 A 383 TYR SER ARG ILE PRO GLN PRO LEU PHE PHE ILE ASN SER SEQRES 22 A 383 GLU TYR PHE GLN TYR PRO ALA ASN ILE ILE LYS MET LYS SEQRES 23 A 383 LYS CYS TYR SER PRO ASP LYS GLU ARG LYS MET ILE THR SEQRES 24 A 383 ILE ARG GLY SER VAL HIS GLN ASN PHE ALA ASP PHE THR SEQRES 25 A 383 PHE ALA THR GLY LYS ILE ILE GLY HIS MET LEU LYS LEU SEQRES 26 A 383 LYS GLY ASP ILE ASP SER ASN VAL ALA ILE ASP LEU SER SEQRES 27 A 383 ASN LYS ALA SER LEU ALA PHE LEU GLN LYS HIS LEU GLY SEQRES 28 A 383 LEU HIS LYS ASP PHE ASP GLN TRP ASP CYS LEU ILE GLU SEQRES 29 A 383 GLY ASP ASP GLU ASN LEU ILE PRO GLY THR ASN ILE ASN SEQRES 30 A 383 THR THR ASN GLN HIS ILE SEQRES 1 B 383 ALA ALA ALA SER PHE GLY GLN THR LYS ILE PRO ARG GLY SEQRES 2 B 383 ASN GLY PRO TYR SER VAL GLY CYS THR ASP LEU MET PHE SEQRES 3 B 383 ASP HIS THR ASN LYS GLY THR PHE LEU ARG LEU TYR TYR SEQRES 4 B 383 PRO SER GLN ASP ASN ASP ARG LEU ASP THR LEU TRP ILE SEQRES 5 B 383 PRO ASN LYS GLU TYR PHE TRP GLY LEU SER LYS PHE LEU SEQRES 6 B 383 GLY THR HIS TRP LEU MET GLY ASN ILE LEU ARG LEU LEU SEQRES 7 B 383 PHE GLY SER MET THR THR PRO ALA ASN TRP ASN SER PRO SEQRES 8 B 383 LEU ARG PRO GLY GLU LYS TYR PRO LEU VAL VAL PHE SER SEQRES 9 B 383 HIS GLY LEU GLY ALA PHE ARG THR LEU TYR SER ALA ILE SEQRES 10 B 383 GLY ILE ASP LEU ALA SER HIS GLY PHE ILE VAL ALA ALA SEQRES 11 B 383 VAL GLU HIS ARG ASP ARG SER ALA SER ALA THR TYR TYR SEQRES 12 B 383 PHE LYS ASP GLN SER ALA ALA GLU ILE GLY ASP LYS SER SEQRES 13 B 383 TRP LEU TYR LEU ARG THR LEU LYS GLN GLU GLU GLU THR SEQRES 14 B 383 HIS ILE ARG ASN GLU GLN VAL ARG GLN ARG ALA LYS GLU SEQRES 15 B 383 CYS SER GLN ALA LEU SER LEU ILE LEU ASP ILE ASP HIS SEQRES 16 B 383 GLY LYS PRO VAL LYS ASN ALA LEU ASP LEU LYS PHE ASP SEQRES 17 B 383 MET GLU GLN LEU LYS ASP SER ILE ASP ARG GLU LYS ILE SEQRES 18 B 383 ALA VAL ILE GLY HIS SER PHE GLY GLY ALA THR VAL ILE SEQRES 19 B 383 GLN THR LEU SER GLU ASP GLN ARG PHE ARG CYS GLY ILE SEQRES 20 B 383 ALA LEU ASP ALA TRP MET PHE PRO LEU GLY ASP GLU VAL SEQRES 21 B 383 TYR SER ARG ILE PRO GLN PRO LEU PHE PHE ILE ASN SER SEQRES 22 B 383 GLU TYR PHE GLN TYR PRO ALA ASN ILE ILE LYS MET LYS SEQRES 23 B 383 LYS CYS TYR SER PRO ASP LYS GLU ARG LYS MET ILE THR SEQRES 24 B 383 ILE ARG GLY SER VAL HIS GLN ASN PHE ALA ASP PHE THR SEQRES 25 B 383 PHE ALA THR GLY LYS ILE ILE GLY HIS MET LEU LYS LEU SEQRES 26 B 383 LYS GLY ASP ILE ASP SER ASN VAL ALA ILE ASP LEU SER SEQRES 27 B 383 ASN LYS ALA SER LEU ALA PHE LEU GLN LYS HIS LEU GLY SEQRES 28 B 383 LEU HIS LYS ASP PHE ASP GLN TRP ASP CYS LEU ILE GLU SEQRES 29 B 383 GLY ASP ASP GLU ASN LEU ILE PRO GLY THR ASN ILE ASN SEQRES 30 B 383 THR THR ASN GLN HIS ILE HET ACT A 11 4 HET ACT A 12 4 HET ACT A 15 4 HET ACT A 16 4 HET ACT A 19 4 HET ACT A 20 4 HET ACT A 22 4 HET ACT A 24 4 HET ACT A 25 4 HET ACT A 28 4 HET ACT A 29 4 HET ACT A 30 4 HET ACT A 32 4 HET ACT A 33 4 HET ACT A 35 4 HET ACT A 36 4 HET ACT A 39 4 HET SO4 B 1 5 HET SO4 B 2 5 HET ACT B 13 4 HET ACT B 14 4 HET ACT B 17 4 HET ACT B 18 4 HET ACT B 21 4 HET ACT B 23 4 HET ACT B 26 4 HET ACT B 27 4 HET ACT B 31 4 HET ACT B 34 4 HET ACT B 37 4 HET ACT B 38 4 HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION FORMUL 3 ACT 29(C2 H3 O2 1-) FORMUL 20 SO4 2(O4 S 2-) FORMUL 34 HOH *511(H2 O) HELIX 1 1 ASN A 100 GLY A 112 1 13 HELIX 2 2 HIS A 114 GLY A 126 1 13 HELIX 3 3 TYR A 160 HIS A 170 1 11 HELIX 4 4 ASP A 192 GLY A 199 1 8 HELIX 5 5 LYS A 210 GLU A 212 5 3 HELIX 6 6 GLU A 213 HIS A 241 1 29 HELIX 7 7 ASP A 254 LYS A 259 5 6 HELIX 8 8 SER A 273 ASP A 286 1 14 HELIX 9 9 GLY A 303 ARG A 309 5 7 HELIX 10 10 TYR A 324 LYS A 333 1 10 HELIX 11 11 VAL A 350 ALA A 360 5 11 HELIX 12 12 GLY A 362 LEU A 369 1 8 HELIX 13 13 ASP A 376 GLY A 397 1 22 HELIX 14 14 ASP A 401 GLN A 404 5 4 HELIX 15 15 TRP A 405 GLU A 410 1 6 HELIX 16 16 ASN B 100 GLY B 112 1 13 HELIX 17 17 TRP B 115 GLY B 126 1 12 HELIX 18 18 TYR B 160 HIS B 170 1 11 HELIX 19 19 ASP B 192 ILE B 198 1 7 HELIX 20 20 LYS B 210 GLU B 212 5 3 HELIX 21 21 GLU B 213 HIS B 241 1 29 HELIX 22 22 ASP B 254 LYS B 259 5 6 HELIX 23 23 SER B 273 ASP B 286 1 14 HELIX 24 24 GLU B 305 ARG B 309 5 5 HELIX 25 25 TYR B 324 CYS B 334 1 11 HELIX 26 26 VAL B 350 ALA B 360 5 11 HELIX 27 27 GLY B 362 LEU B 369 1 8 HELIX 28 28 ASP B 376 GLY B 397 1 22 HELIX 29 29 ASP B 401 GLN B 404 5 4 HELIX 30 30 TRP B 405 GLU B 410 1 6 SHEET 1 A10 ASN A 133 TRP A 134 0 SHEET 2 A10 SER A 64 PHE A 72 1 N VAL A 65 O ASN A 133 SHEET 3 A10 THR A 79 SER A 87 -1 O LEU A 83 N THR A 68 SHEET 4 A10 ILE A 173 VAL A 177 -1 O ALA A 176 N ARG A 82 SHEET 5 A10 TYR A 144 SER A 150 1 N VAL A 147 O ALA A 175 SHEET 6 A10 ILE A 262 HIS A 272 1 O ASP A 263 N TYR A 144 SHEET 7 A10 CYS A 291 LEU A 295 1 O LEU A 295 N GLY A 271 SHEET 8 A10 LEU A 314 SER A 319 1 O PHE A 315 N ALA A 294 SHEET 9 A10 ARG A 341 ILE A 346 1 O LYS A 342 N PHE A 316 SHEET 10 A10 LEU A 416 PRO A 418 -1 O ILE A 417 N THR A 345 SHEET 1 B 2 THR A 95 LEU A 96 0 SHEET 2 B 2 THR A 129 THR A 130 -1 O THR A 130 N THR A 95 SHEET 1 C 2 ALA A 186 TYR A 189 0 SHEET 2 C 2 SER A 202 TYR A 205 -1 O LEU A 204 N THR A 187 SHEET 1 D10 ASN B 133 TRP B 134 0 SHEET 2 D10 VAL B 65 PHE B 72 1 N VAL B 65 O ASN B 133 SHEET 3 D10 THR B 79 PRO B 86 -1 O LEU B 83 N THR B 68 SHEET 4 D10 ILE B 173 VAL B 177 -1 O ALA B 176 N ARG B 82 SHEET 5 D10 TYR B 144 SER B 150 1 N VAL B 147 O ALA B 175 SHEET 6 D10 ILE B 262 HIS B 272 1 O ASP B 263 N TYR B 144 SHEET 7 D10 CYS B 291 LEU B 295 1 O LEU B 295 N GLY B 271 SHEET 8 D10 LEU B 314 SER B 319 1 O PHE B 315 N ALA B 294 SHEET 9 D10 ARG B 341 ILE B 346 1 O ILE B 344 N ASN B 318 SHEET 10 D10 LEU B 416 PRO B 418 -1 O ILE B 417 N THR B 345 SHEET 1 E 2 THR B 95 LEU B 96 0 SHEET 2 E 2 THR B 129 THR B 130 -1 O THR B 130 N THR B 95 SHEET 1 F 2 ALA B 186 TYR B 189 0 SHEET 2 F 2 SER B 202 TYR B 205 -1 O LEU B 204 N THR B 187 CISPEP 1 PHE A 72 ASP A 73 0 -10.74 CISPEP 2 PHE B 72 ASP B 73 0 -12.19 SITE 1 AC1 9 ACT A 15 LYS A 143 HIS A 241 ARG A 264 SITE 2 AC1 9 HOH A 476 SER B 308 ARG B 309 PRO B 311 SITE 3 AC1 9 LYS B 339 SITE 1 AC2 4 SER A 230 GLN A 231 SER A 234 HOH A 494 SITE 1 AC3 5 ACT A 11 LYS A 143 ILE A 262 ASP A 263 SITE 2 AC3 5 ARG A 264 SITE 1 AC4 5 ACT A 28 SER A 202 TRP A 203 TYR B 189 SITE 2 AC4 5 LYS B 191 SITE 1 AC5 5 HIS A 74 ASP A 192 GLN A 193 HOH A 662 SITE 2 AC5 5 HOH A 713 SITE 1 AC6 7 VAL A 245 LYS A 246 ASN A 247 PHE A 253 SITE 2 AC6 7 MET A 255 HOH A 490 HOH A 495 SITE 1 AC7 2 PHE A 72 HOH A 481 SITE 1 AC8 2 LEU A 124 THR A 361 SITE 1 AC9 3 TRP A 298 TYR A 324 HOH A 446 SITE 1 BC1 6 ACT A 16 LYS A 191 HOH A 534 TYR B 189 SITE 2 BC1 6 LYS B 191 HOH B 548 SITE 1 BC2 4 GLU A 305 SER A 308 ARG A 309 ASP B 260 SITE 1 BC3 1 LYS A 246 SITE 1 BC4 2 LYS A 394 HIS A 395 SITE 1 BC5 6 PRO A 57 ARG A 58 ASN A 378 HOH A 548 SITE 2 BC5 6 HOH A 566 HOH A 711 SITE 1 BC6 4 ASN A 378 VAL A 379 ASP A 382 HOH A 510 SITE 1 BC7 3 ARG A 182 HOH A 555 HOH A 700 SITE 1 BC8 7 ASP A 338 GLU A 410 ASP A 412 PRO A 418 SITE 2 BC8 7 HOH A 542 HOH A 635 HOH A 710 SITE 1 BC9 8 LYS A 101 LYS A 201 ARG B 182 ARG B 207 SITE 2 BC9 8 HOH B 471 HOH B 482 HOH B 490 HOH B 496 SITE 1 CC1 6 ASP A 89 ASN A 90 ASN B 100 LYS B 101 SITE 2 CC1 6 HOH B 521 HOH B 634 SITE 1 CC2 3 TRP B 134 LEU B 251 HOH B 518 SITE 1 CC3 5 TYR B 321 PHE B 322 VAL B 350 HIS B 351 SITE 2 CC3 5 HOH B 449 SITE 1 CC4 3 SER B 230 GLN B 231 SER B 234 SITE 1 CC5 3 LYS B 266 LEU B 398 HIS B 399 SITE 1 CC6 4 TRP B 298 PHE B 300 TYR B 324 HOH B 441 SITE 1 CC7 2 LEU B 107 PHE B 357 SITE 1 CC8 3 LYS A 259 HOH A 679 ARG B 309 SITE 1 CC9 3 HIS B 74 ASP B 192 GLN B 193 SITE 1 DC1 1 HOH B 593 SITE 1 DC2 1 PHE B 110 SITE 1 DC3 4 LYS A 370 HOH A 620 ILE B 329 HOH B 639 SITE 1 DC4 3 PRO B 140 ASP B 412 HOH B 594 CRYST1 116.184 83.061 96.705 90.00 115.09 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 0.008607 0.000000 0.004030 0.00000 SCALE2 0.000000 0.012039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011418 0.00000