HEADER HYDROLASE/HYDROLASE INHIBITOR 04-AUG-01 1JQ9 TITLE CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 FROM TITLE 2 DABOIA RUSSELLI PULCHELLA AND A DESIGNED PENTAPEPTIDE PHE-LEU-SER- TITLE 3 TYR-LYS AT 1.8 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.1.4; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PEPTIDE INHIBITOR; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DABOIA RUSSELLII PULCHELLA; SOURCE 3 ORGANISM_TAXID: 97228; SOURCE 4 STRAIN: PULCHELLA; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED. KEYWDS PHOSPHOLIPASE A2, DABOIA RUSSELLI PULCHELLA, NEUROTOXIC, DESIGNED KEYWDS 2 PEPTIDE, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.CHANDRA,J.JASTI,P.KAUR,S.DEY,C.BETZEL,T.P.SINGH REVDAT 6 25-OCT-23 1JQ9 1 REMARK REVDAT 5 23-OCT-19 1JQ9 1 REMARK REVDAT 4 04-OCT-17 1JQ9 1 REMARK REVDAT 3 13-JUL-11 1JQ9 1 VERSN REVDAT 2 24-FEB-09 1JQ9 1 VERSN REVDAT 1 06-NOV-02 1JQ9 0 JRNL AUTH V.CHANDRA,J.JASTI,P.KAUR,S.DEY,M.PERBANDT,A.SRINIVASAN, JRNL AUTH 2 C.BETZEL,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN A SNAKE VENOM JRNL TITL 2 PHOSPHOLIPASE A2 AND A POTENT PEPTIDE INHIBITOR JRNL TITL 3 PHE-LEU-SER-TYR-LYS AT 1.8 A RESOLUTION JRNL REF J.BIOL.CHEM. V. 277 41079 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12186870 JRNL DOI 10.1074/JBC.M206130200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.CHANDRA,P.KAUR,A.SRINIVASAN,T.P.SINGH REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF A PRESYNAPTIC NEUROTOXIC REMARK 1 TITL 2 PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 2.4 REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 296 1117 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.2000.3537 REMARK 1 REFERENCE 2 REMARK 1 AUTH V.CHANDRA,P.KAUR,J.JASTI,C.BETZEL,T.P.SINGH REMARK 1 TITL REGULATION OF CATALYTIC FUNCTION BY MOLECULAR ASSOCIATION: REMARK 1 TITL 2 STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA REMARK 1 TITL 3 (DPLA2) AT 1.9 A RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 1793 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444901014524 REMARK 1 REFERENCE 3 REMARK 1 AUTH V.CHANDRA,J.JASTI,P.KAUR,C.BETZEL,A.SRINIVASAN,T.P.SINGH REMARK 1 TITL FIRST STRUCTURAL EVIDENCE OF A SPECIFIC INHIBITION OF REMARK 1 TITL 2 PHOSPHOLIPASE A2 BY ALPHA-TOCOPHEROL (VITAMIN E) AND ITS REMARK 1 TITL 3 IMPLICATIONS IN INFLAMMATION: CRYSTAL STRUCTURE OF THE REMARK 1 TITL 4 COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ALPHA-TOCOPHEROL REMARK 1 TITL 5 AT 1.8 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 320 215 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1016/S0022-2836(02)00473-4 REMARK 1 REFERENCE 4 REMARK 1 AUTH V.CHANDRA,J.JASTI,P.KAUR,A.SRINIVASAN,C.BETZEL,T.P.SINGH REMARK 1 TITL STRUCTURAL BASIS OF PHOSPHOLIPASE A2 INHIBITION FOR THE REMARK 1 TITL 2 SYNTHESIS OF PROSTAGLANDINS BY THE PLANT ALKALOID REMARK 1 TITL 3 ARISTOLOCHIC ACID FROM A 1.7 A CRYSTAL STRUCTURE REMARK 1 REF BIOCHEMISTRY V. 41 10914 2002 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI0258593 REMARK 1 REFERENCE 5 REMARK 1 AUTH V.CHANDRA,J.JASTI,P.KAUR,S.DEY,A.SRINIVASAN,C.BETZEL, REMARK 1 AUTH 2 T.P.SINGH REMARK 1 TITL DESIGN OF SPECIFIC PEPTIDE INHIBITORS OF PHOSPHOLIPASE A2: REMARK 1 TITL 2 STRUCTURE OF A COMPLEX FORMED BETWEEN RUSSELL'S VIPER REMARK 1 TITL 3 PHOSPHOLIPASE A2 AND A DESIGNED PEPTIDE LEU-ALA-ILE-TYR-SER REMARK 1 TITL 4 (LAIYS) REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1813 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444902013720 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2042260.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 22747 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) : 0.205 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1100 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3708 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 185 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1935 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : 0.83000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : -0.0 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.027 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.400 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) : 1.820 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.320 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 66.05 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 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : PAR.PARAM 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 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : TOP.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE. REMARK 4 REMARK 4 1JQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 239988 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 9.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 4.70000 REMARK 200 R SYM FOR SHELL (I) : 0.09000 REMARK 200 FOR SHELL : 9.900 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: PDB ENTRY 1FE7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM SODIUM CACODYLATE, 1.4M AMMONIUM REMARK 280 SULFATE, 4MM CALCIUM CHLORIDE, 3% DIOXANE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.77400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.77400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.06500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.58050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.06500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.58050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.77400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.06500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.58050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.77400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.06500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.58050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 300 REMARK: THE TWO PROTEIN CHAINS (A AND B) REPRESENT THE TWO REMARK 300 MOLECULES IN THE ASYMMETRIC UNIT, WITH THE A MOLECULE CONTAINING REMARK 300 PEPTIDE INHIBITOR 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: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 -1.000000 0.000000 0.000000 38.06500 REMARK 350 BIOMT2 1 0.000000 -1.000000 0.000000 44.58050 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 38.77400 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 B 372 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLY A 30 CE LYS P 5 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE P 1 C LEU P 2 N 0.301 REMARK 500 LYS P 5 CD LYS P 5 CE -0.298 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 2 CA - CB - CG ANGL. DEV. = 28.6 DEGREES REMARK 500 PHE P 1 CA - C - N ANGL. DEV. = -20.6 DEGREES REMARK 500 PHE P 1 O - C - N ANGL. DEV. = 21.1 DEGREES REMARK 500 LEU P 2 C - N - CA ANGL. DEV. = -20.4 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 SER A 24 22.89 -141.14 REMARK 500 ASP A 39 -166.66 -161.74 REMARK 500 SER B 24 30.28 -144.36 REMARK 500 LEU B 55 67.05 -117.50 REMARK 500 LEU P 2 38.55 -172.20 REMARK 500 TYR P 4 -158.38 -99.87 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 ACY A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN P OF PEPTIDE INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CL5 RELATED DB: PDB REMARK 900 STRUCTURE OF DPLA2 AT 2.45 REMARK 900 RELATED ID: 1FB2 RELATED DB: PDB REMARK 900 STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT REMARK 900 1.95 RESOLUTION REMARK 900 RELATED ID: 1FE7 RELATED DB: PDB REMARK 900 STRUCTURE OF DPLA2 COMPLEXED WITH VITAMIN E REMARK 900 RELATED ID: 1FV0 RELATED DB: PDB REMARK 900 STRUCTURE OF DPLA2 COMPLEXED WITH ARISTOLOCHIC ACID REMARK 900 RELATED ID: 1JQ8 RELATED DB: PDB REMARK 900 STRUCTURE OF DPLA2 COMPLEXED WITH PENTAPEPTIDE LAIYS DBREF 1JQ9 A 1 133 UNP P59071 PA28_DABRP 1 121 DBREF 1JQ9 B 1 133 UNP P59071 PA28_DABRP 1 121 DBREF 1JQ9 P 1 5 PDB 1JQ9 1JQ9 1 5 SEQRES 1 A 121 SER LEU LEU GLU PHE GLY LYS MET ILE LEU GLU GLU THR SEQRES 2 A 121 GLY LYS LEU ALA ILE PRO SER TYR SER SER TYR GLY CYS SEQRES 3 A 121 TYR CYS GLY TRP GLY GLY LYS GLY THR PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 A 121 ASN LEU PRO ASP CYS ASN PRO LYS SER ASP ARG TYR LYS SEQRES 6 A 121 TYR LYS ARG VAL ASN GLY ALA ILE VAL CYS GLU LYS GLY SEQRES 7 A 121 THR SER CYS GLU ASN ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 ALA ALA ILE CYS PHE ARG GLN ASN LEU ASN THR TYR SER SEQRES 9 A 121 LYS LYS TYR MET LEU TYR PRO ASP PHE LEU CYS LYS GLY SEQRES 10 A 121 GLU LEU LYS CYS SEQRES 1 B 121 SER LEU LEU GLU PHE GLY LYS MET ILE LEU GLU GLU THR SEQRES 2 B 121 GLY LYS LEU ALA ILE PRO SER TYR SER SER TYR GLY CYS SEQRES 3 B 121 TYR CYS GLY TRP GLY GLY LYS GLY THR PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 B 121 ASN LEU PRO ASP CYS ASN PRO LYS SER ASP ARG TYR LYS SEQRES 6 B 121 TYR LYS ARG VAL ASN GLY ALA ILE VAL CYS GLU LYS GLY SEQRES 7 B 121 THR SER CYS GLU ASN ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 ALA ALA ILE CYS PHE ARG GLN ASN LEU ASN THR TYR SER SEQRES 9 B 121 LYS LYS TYR MET LEU TYR PRO ASP PHE LEU CYS LYS GLY SEQRES 10 B 121 GLU LEU LYS CYS SEQRES 1 P 5 PHE LEU SER TYR LYS HET ACY A 301 4 HET ACY A 302 4 HET ACY A 304 4 HET ACY B 303 4 HETNAM ACY ACETIC ACID FORMUL 4 ACY 4(C2 H4 O2) FORMUL 8 HOH *279(H2 O) HELIX 1 1 SER A 1 GLY A 14 1 14 HELIX 2 2 LEU A 17 TYR A 22 1 6 HELIX 3 3 ASP A 39 GLY A 53 1 15 HELIX 4 4 THR A 89 ASN A 109 1 21 HELIX 5 5 LEU A 110 TYR A 113 5 4 HELIX 6 6 SER A 114 MET A 118 5 5 HELIX 7 7 PRO A 121 CYS A 126 5 5 HELIX 8 8 SER B 1 GLY B 14 1 14 HELIX 9 9 LEU B 17 TYR B 22 1 6 HELIX 10 10 ASP B 39 ASN B 54 1 16 HELIX 11 11 THR B 89 ASN B 109 1 21 HELIX 12 12 LEU B 110 TYR B 113 5 4 HELIX 13 13 SER B 114 TYR B 117 5 4 HELIX 14 14 PRO B 121 CYS B 126 5 5 SHEET 1 A 2 TYR A 75 VAL A 78 0 SHEET 2 A 2 ALA A 81 CYS A 84 -1 O ALA A 81 N VAL A 78 SHEET 1 B 2 TYR B 75 VAL B 78 0 SHEET 2 B 2 ALA B 81 CYS B 84 -1 O ALA B 81 N VAL B 78 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.03 SSBOND 8 CYS B 27 CYS B 126 1555 1555 2.03 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.04 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.03 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.03 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.03 SSBOND 13 CYS B 61 CYS B 91 1555 1555 2.03 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.03 CISPEP 1 ILE A 19 PRO A 20 0 0.68 CISPEP 2 ILE B 19 PRO B 20 0 0.45 SITE 1 AC1 5 LYS A 116 HOH A 425 GLU B 11 HOH B 379 SITE 2 AC1 5 HOH B 382 SITE 1 AC2 6 PRO A 121 PHE A 124 HOH A 365 ARG B 107 SITE 2 AC2 6 HOH B 369 HOH B 389 SITE 1 AC3 1 SER B 90 SITE 1 AC4 3 ARG A 43 HOH A 330 HOH A 361 SITE 1 AC5 23 LEU A 2 LEU A 3 PHE A 5 GLY A 6 SITE 2 AC5 23 LYS A 7 ILE A 9 ALA A 18 ILE A 19 SITE 3 AC5 23 TYR A 28 CYS A 29 GLY A 30 TRP A 31 SITE 4 AC5 23 GLY A 32 HIS A 48 ASP A 49 LYS A 69 SITE 5 AC5 23 ARG B 43 PHE B 46 VAL B 47 ASN B 54 SITE 6 AC5 23 CYS B 133 HOH B 306 HOH P 64 CRYST1 76.130 89.161 77.548 90.00 90.00 90.00 C 2 2 21 16 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 0.013135 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012895 0.00000