HEADER HYDROLASE 25-APR-04 1T37 TITLE DESIGN OF SPECIFIC INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL STRUCTURE TITLE 2 OF THE COMPLEX FORMED BETWEEN GROUP I PHOSPHOLIPASE A2 AND A DESIGNED TITLE 3 PENTAPEPTIDE LEU-ALA-ILE-TYR-SER AT 2.6A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2 ISOFORM 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE; COMPND 5 EC: 3.1.1.4; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SYNTHETIC PEPTIDE; COMPND 8 CHAIN: P; COMPND 9 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 KEYWDS PHOSPHOLIPASE A2, COMPLEX, INHIBITION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SINGH,N.SINGH,T.JABEEN,J.MAKKER,S.SHARMA,S.DEY,T.P.SINGH REVDAT 6 30-OCT-24 1T37 1 REMARK REVDAT 5 23-AUG-23 1T37 1 REMARK REVDAT 4 27-OCT-21 1T37 1 REMARK SEQADV REVDAT 3 24-FEB-09 1T37 1 VERSN REVDAT 2 20-DEC-05 1T37 1 JRNL REVDAT 1 04-MAY-04 1T37 0 JRNL AUTH R.K.SINGH,N.SINGH,T.JABEEN,S.SHARMA,S.DEY,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF GROUP I PLA2 WITH A JRNL TITL 2 GROUP II-SPECIFIC PEPTIDE LEU-ALA-ILE-TYR-SER (LAIYS) AT 2.6 JRNL TITL 3 A RESOLUTION. JRNL REF J.DRUG TARGET. V. 13 367 2005 JRNL REFN ISSN 1061-186X JRNL PMID 16278156 JRNL DOI 10.1080/10611860500254450 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 721920.770 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 3306 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 SET) : 0.191 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 176 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 399 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 27 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.063 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : 0.90000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.390 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.020 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.950 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 90.34 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ACY.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ACY.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR 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 : 3626 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10800 REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35200 REMARK 200 FOR SHELL : 2.000 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: 1LFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM SODIUM PHOSPHATE BUFFER, 35% REMARK 280 ETHANOL, 2MM CALCIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K 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 32.60150 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 16.30075 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 48.90225 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 APPLY THE FOLLOWING TO CHAINS: A, P 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 ILE P 3 N - CA - C ANGL. DEV. = 18.0 DEGREES REMARK 500 TYR P 4 N - CA - C ANGL. DEV. = -16.4 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 73.96 -154.44 REMARK 500 SER A 34 103.54 76.87 REMARK 500 ASP A 82 31.96 -77.45 REMARK 500 CYS A 119 23.03 174.35 REMARK 500 ILE P 3 158.79 -35.51 REMARK 500 TYR P 4 -103.21 -120.29 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 121 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 122 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 123 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MF4 RELATED DB: PDB REMARK 900 STRUCTURE-BASED DESIGN OF POTENT AND SELECTIVE INHIBITORS OF REMARK 900 PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN REMARK 900 PHOSHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AND A DESIGNED PEPTIDE REMARK 900 INHIBITOR AT 1.9 A RESOLUTION REMARK 900 RELATED ID: 1JQ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 FROM REMARK 900 DABOIA RUSSELLI PULCHELLA AND A DESIGNED PENTAPEPTIDE PHE-LEU-SER- REMARK 900 TYR-LYS AT 1.8 RESOLUTION REMARK 900 RELATED ID: 1SZ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA NAJA REMARK 900 SAGITTIFERA AT 1.5 A RESOLUTION DBREF 1T37 A 1 119 UNP P60045 PA23_NAJSG 8 126 DBREF 1T37 P 1 5 PDB 1T37 1T37 1 5 SEQADV 1T37 ALA A 20 UNP P60045 GLN 26 ENGINEERED MUTATION SEQADV 1T37 THR A 47 UNP P60045 VAL 53 ENGINEERED MUTATION SEQADV 1T37 ASP A 108 UNP P60045 ALA 115 ENGINEERED MUTATION 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 ASP ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS ASN SEQRES 1 P 5 LEU ALA ILE TYR SER HET ACT A 121 4 HET ACT A 122 4 HET ACT A 123 4 HETNAM ACT ACETATE ION FORMUL 3 ACT 3(C2 H3 O2 1-) FORMUL 6 HOH *55(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 ALA A 104 1 21 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 2.03 SSBOND 2 CYS A 27 CYS A 119 1555 1555 2.11 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.04 SSBOND 4 CYS A 44 CYS A 100 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 93 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 86 1555 1555 2.03 SSBOND 7 CYS A 79 CYS A 91 1555 1555 2.03 SITE 1 AC1 3 GLU A 54 LYS A 66 THR A 67 SITE 1 AC2 4 THR A 36 ARG A 62 GLN A 74 HOH A 158 SITE 1 AC3 2 TYR A 3 ASN A 112 CRYST1 42.624 42.624 65.203 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 0.023461 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023461 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015337 0.00000