HEADER HYDROLASE/HYDROLASE INHIBITOR 09-AUG-02 1MF4 TITLE STRUCTURE-BASED DESIGN OF POTENT AND SELECTIVE INHIBITORS OF TITLE 2 PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN TITLE 3 PHOSHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AND A DESIGNED PEPTIDE TITLE 4 INHIBITOR AT 1.9 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VAL-ALA-PHE-ARG-SER; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA SAGITTIFERA; SOURCE 3 ORGANISM_TAXID: 195058; SOURCE 4 SECRETION: VENOM; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS NAJA NAJA SAGITTIFERA, PHOSPHOLIPASE A2, DESIGNED INHIBITOR, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SINGH,P.VIKRAM,M.PARAMSIVAM,T.JABEEN,S.SHARMA,J.MAKKER,S.DEY, AUTHOR 2 P.KAUR,A.SRINIVASAN,T.P.SINGH REVDAT 6 13-NOV-24 1MF4 1 REMARK LINK REVDAT 5 13-JUL-11 1MF4 1 VERSN REVDAT 4 24-FEB-09 1MF4 1 VERSN REVDAT 3 30-JAN-07 1MF4 2 AUTHOR REVDAT 2 23-DEC-03 1MF4 1 JRNL REVDAT 1 30-SEP-03 1MF4 0 JRNL AUTH R.K.SINGH,P.VIKRAM,J.MAKKER,T.JABEEN,S.SHARMA,S.DEY,P.KAUR, JRNL AUTH 2 A.SRINIVASAN,T.P.SINGH JRNL TITL DESIGN OF SPECIFIC PEPTIDE INHIBITORS FOR GROUP I JRNL TITL 2 PHOSPHOLIPASE A2: STRUCTURE OF A COMPLEX FORMED BETWEEN JRNL TITL 3 PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA (GROUP I) AND A JRNL TITL 4 DESIGNED PEPTIDE INHIBITOR VAL-ALA-PHE-ARG-SER (VAFRS) AT JRNL TITL 5 1.9 A RESOLUTION REVEALS UNIQUE FEATURES JRNL REF BIOCHEMISTRY V. 42 11701 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 14529280 JRNL DOI 10.1021/BI035076X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.K.SINGH,S.SHARMA,T.JABEEN,P.KAUR,T.P.SINGH REMARK 1 TITL CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA REMARK 1 TITL 2 NAJA SAGITTIFERA AT 1.5 A RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH R.K.SINGH,P.VIKRAM,M.PARAMASIVAM,T.JABEEN,S.SHARMA,P.KAUR, REMARK 1 AUTH 2 A.SRINIVASAN,T.P.SINGH REMARK 1 TITL CRYSTAL STRUCTURE OF A NEW ISOFORM OF PHOSPHOLIPASE A2 FROM REMARK 1 TITL 2 NAJA NAJA SAGITTIFERA AT 1.6 A RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8247 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 411 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 314 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : 0.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.811 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 975 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1322 ; 1.748 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 121 ; 3.468 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;17.004 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 151 ;17.004 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 135 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 773 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 456 ; 0.292 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 82 ; 0.167 ; 0.500 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): 52 ; 0.449 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.689 ; 0.500 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): 613 ; 0.880 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 971 ; 1.769 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 362 ; 2.472 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 351 ; 3.903 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1MF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016865. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 290.0 REMARK 200 PH : 6.00 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE CRYSTAL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8247 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 1.040 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28900 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1LN8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM PHOSPHATE, CACL2, ETHANOL; CO REMARK 280 -CRYSTALLATION OF PROTEIN: PEPTIDE IN 1:10 MOLAR RATIO, PH 6.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 32.93300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.46650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.39950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 LYS A 6 CG - CD - CE ANGL. DEV. = 30.9 DEGREES REMARK 500 ASP A 94 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 PHE B 3 CB - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 PHE B 3 CB - CG - CD2 ANGL. DEV. = -4.3 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 ASP A 24 77.44 -156.11 REMARK 500 LYS A 31 -84.13 -116.05 REMARK 500 ASP A 82 37.16 -90.91 REMARK 500 ALA B 2 -64.40 -127.32 REMARK 500 PHE B 3 -168.19 -167.45 REMARK 500 REMARK 500 REMARK: NULL 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 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 28 O REMARK 620 2 LYS A 31 O 112.3 REMARK 620 3 GLY A 32 O 73.8 56.7 REMARK 620 4 ASP A 49 OD2 64.4 140.7 87.0 REMARK 620 5 ASP A 49 OD1 76.2 170.9 131.2 45.1 REMARK 620 6 HOH A 244 O 156.7 54.2 83.1 112.3 119.0 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF VAL-ALA-PHE-ARG-SER REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LFF RELATED DB: PDB REMARK 900 1LFF IS THE CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM REMARK 900 NAJA NAJA SAGITTIFERA AT 1.5 A RESOLUTION REMARK 900 RELATED ID: 1LN8 RELATED DB: PDB REMARK 900 1LN8 IS THE CRYSTAL STRUCTURE OF A NEW ISOFORM OF PHOSPHOLIPASE A2 REMARK 900 FROM NAJA NAJA SAGITTIFERA AT 1.6 A RESOLUTION DBREF 1MF4 A 1 120 UNP P60045 PA23_NAJSG 8 126 DBREF 1MF4 B 1 5 PDB 1MF4 1MF4 1 5 SEQRES 1 A 119 ASN LEU TYR GLN PHE LYS ASN MET ILE GLN CYS THR VAL SEQRES 2 A 119 PRO SER ARG SER TRP ALA ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY LYS GLY GLY SER GLY THR PRO VAL ASP ASP SEQRES 4 A 119 LEU ASP ARG CYS CYS GLN THR HIS ASP ASN CYS TYR ASN SEQRES 5 A 119 GLU ALA GLU ASN ILE SER GLY CYS ARG PRO TYR PHE LYS SEQRES 6 A 119 THR TYR SER TYR GLU CYS THR GLN GLY THR LEU THR CYS SEQRES 7 A 119 LYS GLY ASP ASN ASN ALA CYS ALA ALA SER VAL CYS ASP SEQRES 8 A 119 CYS ASP ARG LEU ALA ALA ILE CYS PHE ALA GLY ALA PRO SEQRES 9 A 119 TYR ASN ASP ALA ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS ASN SEQRES 1 B 5 VAL ALA PHE ARG SER HET CA A 201 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ FORMUL 4 HOH *105(H2 O) HELIX 1 1 ASN A 1 VAL A 13 1 13 HELIX 2 2 SER A 18 ALA A 23 5 6 HELIX 3 3 ASP A 39 GLU A 56 1 18 HELIX 4 4 ASN A 84 GLY A 103 1 20 HELIX 5 5 ASN A 107 TYR A 111 5 5 HELIX 6 6 ASP A 114 CYS A 119 1 6 SHEET 1 A 2 TYR A 70 THR A 73 0 SHEET 2 A 2 THR A 76 CYS A 79 -1 O THR A 78 N GLU A 71 SSBOND 1 CYS A 11 CYS A 72 1555 1555 2.06 SSBOND 2 CYS A 27 CYS A 119 1555 1555 2.02 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.05 SSBOND 4 CYS A 44 CYS A 100 1555 1555 2.01 SSBOND 5 CYS A 51 CYS A 93 1555 1555 2.02 SSBOND 6 CYS A 61 CYS A 86 1555 1555 2.01 SSBOND 7 CYS A 79 CYS A 91 1555 1555 2.02 LINK O TYR A 28 CA CA A 201 1555 1555 2.76 LINK O LYS A 31 CA CA A 201 1555 1555 2.56 LINK O GLY A 32 CA CA A 201 1555 1555 2.44 LINK OD2 ASP A 49 CA CA A 201 1555 1555 2.52 LINK OD1 ASP A 49 CA CA A 201 1555 1555 3.00 LINK CA CA A 201 O HOH A 244 1555 1555 2.58 SITE 1 AC1 6 TYR A 28 LYS A 31 GLY A 32 ASP A 49 SITE 2 AC1 6 HOH A 244 ARG B 4 SITE 1 AC2 20 PHE A 5 LYS A 6 ILE A 9 TRP A 19 SITE 2 AC2 20 PHE A 22 ALA A 23 TYR A 28 GLY A 30 SITE 3 AC2 20 LYS A 31 ASP A 40 ARG A 43 CYS A 44 SITE 4 AC2 20 CYS A 45 THR A 47 HIS A 48 ASP A 49 SITE 5 AC2 20 TYR A 64 CYS A 100 CA A 201 HOH B 88 CRYST1 42.779 42.779 65.866 90.00 90.00 90.00 P 41 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 0.023376 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023376 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015182 0.00000