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HEADER HYDROLASE 16-MAY-08 3D5E
TITLE CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING
TITLE 2 FACTOR ACETYLHYDROLASE COVALENTLY INHIBITED BY PARAOXON
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-
COMPND 6 ASSOCIATED PHOSPHOLIPASE A2, LDL-PLA(2), 2-ACETYL-1-
COMPND 7 ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE, 1-ALKYL-2-
COMPND 8 ACETYLGLYCEROPHOSPHOCHOLINE ESTERASE;
COMPND 9 EC: 3.1.1.47;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 GENE: PLA2G7, PAFAH;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE, SECRETED
KEYWDS 2 PROTEIN, ALPHA/BETA-HYDROLASE-FOLD, LDL-BOUND; LIPOPROTEIN
KEYWDS 3 ASSOCIATED PHOSPHOLIPASE A2, LP-PLA2, GROUP VIIA PLA2,
KEYWDS 4 GLYCOPROTEIN, HYDROLASE, LIPID DEGRADATION, POLYMORPHISM,
KEYWDS 5 SECRETED, PARAOXON
EXPDTA X-RAY DIFFRACTION
AUTHOR U.SAMANTA,B.J.BAHNSON
REVDAT 1 09-SEP-08 3D5E 0
JRNL AUTH U.SAMANTA,B.J.BAHNSON
JRNL TITL CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET
JRNL TITL 2 ACTIVATING FACTOR ACETYLHYDROLASE: STRUCTURAL
JRNL TITL 3 IMPLICATION TO LIPOPROTEIN BINDING AND CATALYSIS.
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9
REMARK 3 NUMBER OF REFLECTIONS : 45723
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) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.204
REMARK 3 FREE R VALUE : 0.261
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2439
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2560
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.99
REMARK 3 BIN R VALUE (WORKING SET) : 0.2100
REMARK 3 BIN FREE R VALUE SET COUNT : 146
REMARK 3 BIN FREE R VALUE : 0.3300
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 ALL ATOMS : 6365
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.12000
REMARK 3 B22 (A**2) : 0.38000
REMARK 3 B33 (A**2) : -0.51000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.05000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.249
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.980
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6224 ; 0.023 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8391 ; 1.905 ; 1.952
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 745 ; 7.414 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 301 ;39.843 ;23.920
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1080 ;17.460 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;15.648 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 894 ; 0.130 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4709 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2759 ; 0.209 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4145 ; 0.309 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 356 ; 0.178 ; 0.200
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): 73 ; 0.232 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.082 ; 0.200
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): 3882 ; 1.604 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5985 ; 2.069 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2733 ; 3.385 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2406 ; 4.917 ; 4.500
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 : 0
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 0
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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
REMARK 3 RIDING POSITIONS
REMARK 4
REMARK 4 3D5E COMPLIES WITH FORMAT V. 3.1, 01-AUG-2007
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB.
REMARK 100 THE RCSB ID CODE IS RCSB047613.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-MAR-2006
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X29A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.072
REMARK 200 MONOCHROMATOR : SI(111) ROSENBAUM-ROCK
REMARK 200 OPTICS : SI(111) ROSENBAUM-ROCK
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000
REMARK 200 DATA SCALING SOFTWARE : HKL2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48162
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
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 (%) : 94.9
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : 0.05300
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 19.5900
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) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 73.8
REMARK 200 DATA REDUNDANCY IN SHELL : 2.10
REMARK 200 R MERGE FOR SHELL (I) : 0.19300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 3.430
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP OF CCP4I, REFMAC5 OF CCP4I FOR FINAL
REMARK 200 REFINEMENT
REMARK 200 STARTING MODEL: NATIVE STRUCTURE, PDB ENTRY 3D59
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 7.0, VAPOR DIFFUSION, HANGING
REMARK 280 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 1/2+X,1/2+Y,Z
REMARK 290 4555 1/2-X,1/2+Y,-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 58.60650
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.34800
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.60650
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.34800
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 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; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSEQI
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 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 THR B 424
REMARK 465 THR B 425
REMARK 465 ASN B 426
REMARK 465 GLN B 427
REMARK 465 HIS B 428
REMARK 465 ILE B 429
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 -170.71 -69.72
REMARK 500 ASP A 89 152.94 177.90
REMARK 500 ASP A 91 -82.52 -20.43
REMARK 500 THR A 113 -164.78 -115.38
REMARK 500 ALA A 155 -159.30 -97.93
REMARK 500 PHE A 156 -178.89 -173.83
REMARK 500 LEU A 209 -166.42 -106.96
REMARK 500 SER A 273 -104.57 63.44
REMARK 500 ASN B 90 14.33 -148.76
REMARK 500 ASP B 91 -73.78 -54.84
REMARK 500 THR B 113 -162.42 -106.12
REMARK 500 HIS B 114 -152.75 -150.49
REMARK 500 ALA B 155 -162.85 -106.77
REMARK 500 LYS B 266 73.72 -109.33
REMARK 500 SER B 273 -105.77 60.97
REMARK 500 ILE B 422 170.30 -53.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 SITE_DESCRIPTION: DEP BINDING SITE FOR RESIDUE A 473
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 SITE_DESCRIPTION: DEP BINDING SITE FOR RESIDUE B 473
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 1
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE A 3
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE A 4
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE A 5
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 6
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 7
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 8
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 9
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 10
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE A 11
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE A 12
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 13
REMARK 800 SITE_IDENTIFIER: BC6
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 14
REMARK 800 SITE_IDENTIFIER: BC7
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE B 15
REMARK 800 SITE_IDENTIFIER: BC8
REMARK 800 SITE_DESCRIPTION: FMT BINDING SITE FOR RESIDUE A 16
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3D59 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING
REMARK 900 FACTOR ACETYLHYDROLASE
DBREF 3D5E A 47 429 UNP Q13093 PAFA_HUMAN 47 429
DBREF 3D5E 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 DEP A 473 8
HET FMT A 2 3
HET FMT A 3 3
HET FMT A 4 3
HET FMT A 5 3
HET FMT A 11 3
HET FMT A 12 3
HET FMT A 16 3
HET DEP B 473 8
HET FMT B 1 3
HET FMT B 6 3
HET FMT B 7 3
HET FMT B 8 3
HET FMT B 9 3
HET FMT B 10 3
HET FMT B 13 3
HET FMT B 14 3
HET FMT B 15 3
HETNAM DEP DIETHYL PHOSPHONATE
HETNAM FMT FORMIC ACID
FORMUL 3 DEP 2(C4 H11 O3 P)
FORMUL 4 FMT 16(C H2 O2)
FORMUL 21 HOH *288(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 ILE A 198 1 7
HELIX 5 5 GLU A 213 HIS A 241 1 29
HELIX 6 6 ASP A 254 LYS A 259 5 6
HELIX 7 7 SER A 273 ASP A 286 1 14
HELIX 8 8 GLU A 305 ARG A 309 5 5
HELIX 9 9 TYR A 324 CYS A 334 1 11
HELIX 10 10 VAL A 350 ALA A 360 5 11
HELIX 11 11 GLY A 362 LEU A 369 1 8
HELIX 12 12 ASP A 376 GLY A 397 1 22
HELIX 13 13 ASP A 401 GLN A 404 5 4
HELIX 14 14 TRP A 405 GLU A 410 1 6
HELIX 15 15 ASN B 100 GLY B 112 1 13
HELIX 16 16 HIS B 114 GLY B 126 1 13
HELIX 17 17 TYR B 160 HIS B 170 1 11
HELIX 18 18 ASP B 192 GLY B 199 1 8
HELIX 19 19 LYS B 210 GLU B 212 5 3
HELIX 20 20 GLU B 213 HIS B 241 1 29
HELIX 21 21 ASP B 254 LYS B 259 5 6
HELIX 22 22 SER B 273 ASP B 286 1 14
HELIX 23 23 GLY B 303 ARG B 309 5 7
HELIX 24 24 TYR B 324 CYS B 334 1 11
HELIX 25 25 VAL B 350 ALA B 360 5 11
HELIX 26 26 GLY B 362 LEU B 369 1 8
HELIX 27 27 ASP B 376 GLY B 397 1 22
HELIX 28 28 ASP B 401 GLN B 404 5 4
HELIX 29 29 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 THR A 79 N PHE A 72
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 ILE A 270 N VAL A 148
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 ILE A 344 N ASN A 318
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 SER A 202 N TYR A 189
SHEET 1 D10 ASN B 133 TRP B 134 0
SHEET 2 D10 SER B 64 PHE B 72 1 N VAL B 65 O ASN B 133
SHEET 3 D10 THR B 79 SER B 87 -1 O SER B 87 N SER B 64
SHEET 4 D10 ILE B 173 VAL B 177 -1 O VAL B 174 N TYR B 84
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 ILE B 270 N VAL B 148
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 ILE B 317 N ALA B 294
SHEET 9 D10 ARG B 341 ILE B 346 1 O ILE B 346 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 SER B 202 N TYR B 189
LINK OG SER A 273 P DEP A 473 1555 1555 1.69
LINK OG SER B 273 P DEP B 473 1555 1555 1.75
CISPEP 1 PHE A 72 ASP A 73 0 -6.94
CISPEP 2 PHE B 72 ASP B 73 0 -6.50
SITE 1 AC1 7 GLY A 152 LEU A 153 SER A 273 PHE A 274
SITE 2 AC1 7 TRP A 298 PHE A 322 HIS A 351
SITE 1 AC2 4 ASN A 135 LYS A 252 ASP A 254 GLN A 257
SITE 1 AC3 4 GLU A 256 GLN A 257 LYS A 259 HOH A 509
SITE 1 AC4 4 PHE A 300 ALA A 326 LYS A 330 HOH A 528
SITE 1 AC5 3 THR A 54 MET A 128 THR A 129
SITE 1 AC6 2 ASP A 382 LYS A 386
SITE 1 AC7 2 ARG A 182 THR A 208
SITE 1 AC8 7 GLY B 152 LEU B 153 SER B 273 PHE B 274
SITE 2 AC8 7 TRP B 298 HIS B 351 GLN B 352
SITE 1 AC9 2 TRP B 298 TYR B 324
SITE 1 BC1 4 TYR B 335 LYS B 342 MET B 343 HOH B 518
SITE 1 BC2 4 ARG B 182 TRP B 203 LEU B 204 TYR B 205
SITE 1 BC3 5 SER B 230 GLN B 231 SER B 234 ARG B 288
SITE 2 BC3 5 HOH B 554
SITE 1 BC4 6 ILE A 422 ASN A 423 GLU B 320 GLN B 323
SITE 2 BC4 6 ASN B 421 ILE B 422
SITE 1 BC5 4 PRO B 57 ARG B 58 ALA B 162 ASP B 166
SITE 1 BC6 6 PRO A 311 LYS B 143 ILE B 262 ARG B 264
SITE 2 BC6 6 HOH B 605 HOH B 606
SITE 1 BC7 3 SER B 234 ARG B 288 HOH B 590
SITE 1 BC8 4 GLN B 393 LYS B 394 ASP B 403 HOH B 498
CRYST1 117.213 78.696 97.340 90.00 101.61 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 0.008531 0.000000 0.001753 0.00000
SCALE2 0.000000 0.012707 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010488 0.00000
TER 3029 ASN A 426
TER 6015 ASN B 423
MASTER 342 0 18 29 28 0 22 6 6365 2 66 60
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