| 5jap-pdb | HEADER HYDROLASE 12-APR-16 5JAP
TITLE EXPLOITATION OF A NOVEL BINDING POCKET IN HUMAN LIPOPROTEIN-ASSOCIATED
TITLE 2 PHOSPHOLIPASE A2 (LP-PLA2) DISCOVERED THROUGH X-RAY
TITLE 3 FRAGMENT SCREENING
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PAF ACETYLHYDROLASE,1-ALKYL-2-ACETYLGLYCEROPHOSPHOCHOLINE
COMPND 5 ESTERASE,2-ACETYL-1-ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE,GROUP-VIIA
COMPND 6 PHOSPHOLIPASE A2,GVIIA-PLA2,LDL-ASSOCIATED PHOSPHOLIPASE A2,LDL-
COMPND 7 PLA(2),PAF 2-ACYLHYDROLASE;
COMPND 8 EC: 3.1.1.47;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PLA2G7, PAFAH;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PHOSPHOLIPASE, LIPID METABOLISM, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.J.DAY
REVDAT 1 25-MAY-16 5JAP 0
JRNL AUTH A.J.WOOLFORD,J.E.PERO,S.ARAVAPALLI,V.BERDINI,J.E.COYLE,
JRNL AUTH 2 P.J.DAY,A.M.DODSON,P.GRONDIN,F.P.HOLDING,L.Y.LEE,P.LI,
JRNL AUTH 3 E.S.MANAS,J.P.MARINO,A.C.MARTIN,B.W.MCCLELAND,R.L.MCMENAMIN,
JRNL AUTH 4 C.W.MURRAY,C.E.NEIPP,L.W.PAGE,V.K.PATEL,F.POTVAIN,S.J.RICH,
JRNL AUTH 5 R.A.RIVERO,K.SMITH,D.O.SOMERS,L.TROTTET,R.VELAGALETI,
JRNL AUTH 6 G.WILLIAMS,R.XIE
JRNL TITL EXPLOITATION OF A NOVEL BINDING POCKET IN HUMAN
JRNL TITL 2 LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2 (LP-PLA2) DISCOVERED
JRNL TITL 3 THROUGH X-RAY FRAGMENT SCREENING.
JRNL REF J.MED.CHEM. 2016
JRNL REFN ISSN 0022-2623
JRNL PMID 27167608
JRNL DOI 10.1021/ACS.JMEDCHEM.6B00212
REMARK 2
REMARK 2 RESOLUTION. 2.46 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.6
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.46
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.24
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 15287
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) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.173
REMARK 3 FREE R VALUE : 0.246
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 779
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.46
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.63
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.07
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL
REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2624
REMARK 3 BIN R VALUE (WORKING SET) : 0.2290
REMARK 3 BIN FREE R VALUE : 0.3470
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.89
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 135
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2973
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 27
REMARK 3 SOLVENT ATOMS : 365
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 49.77
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.33
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.94620
REMARK 3 B22 (A**2) : -7.57940
REMARK 3 B33 (A**2) : 5.63320
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -2.08620
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.260
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 1.042
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.292
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.595
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.285
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 3097 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 4203 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1075 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 77 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 462 ; 16.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 3097 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 392 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 3856 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.011
REMARK 3 BOND ANGLES (DEGREES) : 1.08
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 6.90
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.04
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|55 - A|425 }
REMARK 3 ORIGIN FOR THE GROUP (A): 30.5112 14.8788 0.9311
REMARK 3 T TENSOR
REMARK 3 T11: -0.2083 T22: -0.1154
REMARK 3 T33: -0.0039 T12: 0.0075
REMARK 3 T13: 0.0070 T23: -0.0279
REMARK 3 L TENSOR
REMARK 3 L11: 1.7389 L22: 1.8287
REMARK 3 L33: 1.3643 L12: 0.0906
REMARK 3 L13: 0.3296 L23: -0.2717
REMARK 3 S TENSOR
REMARK 3 S11: 0.0379 S12: -0.0693 S13: 0.0314
REMARK 3 S21: 0.0570 S22: -0.0485 S23: 0.0975
REMARK 3 S31: -0.0388 S32: -0.0345 S33: 0.0106
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5JAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-16.
REMARK 100 THE DEPOSITION ID IS D_1000220265.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-JUN-11
REMARK 200 TEMPERATURE (KELVIN) : 93
REMARK 200 PH : 7.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15287
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460
REMARK 200 RESOLUTION RANGE LOW (A) : 44.240
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 2.800
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 9.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.69
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 28.0%W/V PEG 3350, 0.1M
REMARK 280 HEPES/NAOHPH=7.4, 1.3M NACL, PH 7.4, VAPOR DIFFUSION, SITTING
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 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 49.96350
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.33050
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.96350
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.33050
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: 440 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15050 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 CA CA A 501 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 678 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 868 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 939 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 MET 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 GLN A 53
REMARK 465 THR A 54
REMARK 465 ASN A 426
REMARK 465 GLN A 427
REMARK 465 HIS A 428
REMARK 465 HIS A 429
REMARK 465 HIS A 430
REMARK 465 HIS A 431
REMARK 465 HIS A 432
REMARK 465 HIS A 433
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 241 CG ND1 CD2 CE1 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 -168.17 -77.00
REMARK 500 PHE A 156 -177.63 -176.30
REMARK 500 LEU A 206 133.79 -39.66
REMARK 500 SER A 273 -108.62 68.66
REMARK 500 THR A 424 -124.07 -112.44
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 965 DISTANCE = 7.22 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 501 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 285 O
REMARK 620 2 HOH A 680 O 67.6
REMARK 620 3 HOH A 868 O 112.5 88.9
REMARK 620 4 GLU A 285 O 0.0 67.6 112.5
REMARK 620 5 HOH A 680 O 113.3 177.7 88.7 113.3
REMARK 620 6 HOH A 868 O 112.5 88.9 0.0 112.5 88.8
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 6HZ A 504
DBREF 5JAP A 46 428 UNP Q13093 PAFA_HUMAN 46 428
SEQADV 5JAP HIS A 429 UNP Q13093 EXPRESSION TAG
SEQADV 5JAP HIS A 430 UNP Q13093 EXPRESSION TAG
SEQADV 5JAP HIS A 431 UNP Q13093 EXPRESSION TAG
SEQADV 5JAP HIS A 432 UNP Q13093 EXPRESSION TAG
SEQADV 5JAP HIS A 433 UNP Q13093 EXPRESSION TAG
SEQRES 1 A 388 MET ALA ALA ALA SER PHE GLY GLN THR LYS ILE PRO ARG
SEQRES 2 A 388 GLY ASN GLY PRO TYR SER VAL GLY CYS THR ASP LEU MET
SEQRES 3 A 388 PHE ASP HIS THR ASN LYS GLY THR PHE LEU ARG LEU TYR
SEQRES 4 A 388 TYR PRO SER GLN ASP ASN ASP ARG LEU ASP THR LEU TRP
SEQRES 5 A 388 ILE PRO ASN LYS GLU TYR PHE TRP GLY LEU SER LYS PHE
SEQRES 6 A 388 LEU GLY THR HIS TRP LEU MET GLY ASN ILE LEU ARG LEU
SEQRES 7 A 388 LEU PHE GLY SER MET THR THR PRO ALA ASN TRP ASN SER
SEQRES 8 A 388 PRO LEU ARG PRO GLY GLU LYS TYR PRO LEU VAL VAL PHE
SEQRES 9 A 388 SER HIS GLY LEU GLY ALA PHE ARG THR LEU TYR SER ALA
SEQRES 10 A 388 ILE GLY ILE ASP LEU ALA SER HIS GLY PHE ILE VAL ALA
SEQRES 11 A 388 ALA VAL GLU HIS ARG ASP ARG SER ALA SER ALA THR TYR
SEQRES 12 A 388 TYR PHE LYS ASP GLN SER ALA ALA GLU ILE GLY ASP LYS
SEQRES 13 A 388 SER TRP LEU TYR LEU ARG THR LEU LYS GLN GLU GLU GLU
SEQRES 14 A 388 THR HIS ILE ARG ASN GLU GLN VAL ARG GLN ARG ALA LYS
SEQRES 15 A 388 GLU CYS SER GLN ALA LEU SER LEU ILE LEU ASP ILE ASP
SEQRES 16 A 388 HIS GLY LYS PRO VAL LYS ASN ALA LEU ASP LEU LYS PHE
SEQRES 17 A 388 ASP MET GLU GLN LEU LYS ASP SER ILE ASP ARG GLU LYS
SEQRES 18 A 388 ILE ALA VAL ILE GLY HIS SER PHE GLY GLY ALA THR VAL
SEQRES 19 A 388 ILE GLN THR LEU SER GLU ASP GLN ARG PHE ARG CYS GLY
SEQRES 20 A 388 ILE ALA LEU ASP ALA TRP MET PHE PRO LEU GLY ASP GLU
SEQRES 21 A 388 VAL TYR SER ARG ILE PRO GLN PRO LEU PHE PHE ILE ASN
SEQRES 22 A 388 SER GLU TYR PHE GLN TYR PRO ALA ASN ILE ILE LYS MET
SEQRES 23 A 388 LYS LYS CYS TYR SER PRO ASP LYS GLU ARG LYS MET ILE
SEQRES 24 A 388 THR ILE ARG GLY SER VAL HIS GLN ASN PHE ALA ASP PHE
SEQRES 25 A 388 THR PHE ALA THR GLY LYS ILE ILE GLY HIS MET LEU LYS
SEQRES 26 A 388 LEU LYS GLY ASP ILE ASP SER ASN VAL ALA ILE ASP LEU
SEQRES 27 A 388 SER ASN LYS ALA SER LEU ALA PHE LEU GLN LYS HIS LEU
SEQRES 28 A 388 GLY LEU HIS LYS ASP PHE ASP GLN TRP ASP CYS LEU ILE
SEQRES 29 A 388 GLU GLY ASP ASP GLU ASN LEU ILE PRO GLY THR ASN ILE
SEQRES 30 A 388 ASN THR THR ASN GLN HIS HIS HIS HIS HIS HIS
HET CA A 501 1
HET CL A 502 1
HET DMS A 503 4
HET 6HZ A 504 40
HETNAM CA CALCIUM ION
HETNAM CL CHLORIDE ION
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM 6HZ (2,5-DIHYDRO-1H-PYRROL-1-YL)(2',6-DIMETHYL[1,1'-
HETNAM 2 6HZ BIPHENYL]-3-YL)METHANONE
FORMUL 2 CA CA 2+
FORMUL 3 CL CL 1-
FORMUL 4 DMS C2 H6 O S
FORMUL 5 6HZ C19 H19 N O
FORMUL 6 HOH *365(H2 O)
HELIX 1 AA1 ASN A 100 GLY A 112 1 13
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 ILE A 198 1 7
HELIX 5 AA5 GLU A 213 HIS A 241 1 29
HELIX 6 AA6 ASP A 254 LYS A 259 5 6
HELIX 7 AA7 SER A 273 ASP A 286 1 14
HELIX 8 AA8 GLU A 305 ARG A 309 5 5
HELIX 9 AA9 TYR A 324 LYS A 333 1 10
HELIX 10 AB1 VAL A 350 PHE A 359 5 10
HELIX 11 AB2 GLY A 362 LEU A 369 1 8
HELIX 12 AB3 ASP A 376 GLY A 397 1 22
HELIX 13 AB4 ASP A 401 GLN A 404 5 4
HELIX 14 AB5 TRP A 405 GLU A 410 1 6
SHEET 1 AA111 ASP A 94 LEU A 96 0
SHEET 2 AA111 THR A 129 TRP A 134 -1 O THR A 130 N THR A 95
SHEET 3 AA111 SER A 64 PHE A 72 1 N VAL A 65 O ASN A 133
SHEET 4 AA111 THR A 79 SER A 87 -1 O LEU A 81 N LEU A 70
SHEET 5 AA111 ILE A 173 VAL A 177 -1 O VAL A 174 N TYR A 84
SHEET 6 AA111 TYR A 144 SER A 150 1 N VAL A 147 O ALA A 175
SHEET 7 AA111 ILE A 262 HIS A 272 1 O ASP A 263 N TYR A 144
SHEET 8 AA111 CYS A 291 LEU A 295 1 O LEU A 295 N GLY A 271
SHEET 9 AA111 LEU A 314 SER A 319 1 O PHE A 315 N ALA A 294
SHEET 10 AA111 ARG A 341 ILE A 346 1 O ILE A 344 N ASN A 318
SHEET 11 AA111 LEU A 416 PRO A 418 -1 O ILE A 417 N THR A 345
SHEET 1 AA2 2 ALA A 186 TYR A 189 0
SHEET 2 AA2 2 SER A 202 TYR A 205 -1 O SER A 202 N TYR A 189
LINK O GLU A 285 CA CA A 501 1555 1555 2.49
LINK CA CA A 501 O HOH A 680 1555 1555 2.44
LINK CA CA A 501 O HOH A 868 1555 1555 2.53
LINK O GLU A 285 CA CA A 501 1555 2655 2.49
LINK CA CA A 501 O HOH A 680 1555 2655 2.45
LINK CA CA A 501 O HOH A 868 1555 2655 2.53
CISPEP 1 PHE A 72 ASP A 73 0 -5.45
SITE 1 AC1 3 GLU A 285 HOH A 680 HOH A 868
SITE 1 AC2 3 HIS A 351 LYS A 370 HOH A 944
SITE 1 AC3 7 ASP A 89 LEU A 153 SER A 273 TRP A 298
SITE 2 AC3 7 PHE A 322 HIS A 351 HOH A 619
SITE 1 AC4 7 PHE A 110 LEU A 111 GLY A 154 GLN A 352
SITE 2 AC4 7 PHE A 357 LEU A 371 HOH A 685
CRYST1 99.927 90.661 51.303 90.00 111.55 90.00 C 1 2 1 4
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 0.010007 0.000000 0.003952 0.00000
SCALE2 0.000000 0.011030 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020957 0.00000
TER 2979 THR A 425
MASTER 342 0 4 14 13 0 6 6 3365 1 48 30
END
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