10 20 30 40 50 60 70 80 1JQ8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/HYDROLASE INHIBITOR 04-AUG-01 1JQ8
TITLE DESIGN OF SPECIFIC INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL STRUCTURE TITLE 2 OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI TITLE 3 PULCHELLA AND A DESIGNED PENTAPEPTIDE LEU-ALA-ILE-TYR-SER AT 2.0 TITLE 4 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 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED.
KEYWDS NEUROTOXIC, DESIGNED PEPTIDE, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR V.CHANDRA,J.JASTI,P.KAUR,S.DEY,C.BETZEL,T.P.SINGH
REVDAT 4 16-NOV-11 1JQ8 1 HETATM REVDAT 3 13-JUL-11 1JQ8 1 VERSN REVDAT 2 24-FEB-09 1JQ8 1 VERSN REVDAT 1 06-NOV-02 1JQ8 0
JRNL AUTH V.CHANDRA,J.JASTI,P.KAUR,S.DEY,A.SRINIVASAN,C.H.BETZEL, JRNL AUTH 2 T.P.SINGH JRNL TITL DESIGN OF SPECIFIC PEPTIDE INHIBITORS OF PHOSPHOLIPASE A2: JRNL TITL 2 STRUCTURE OF A COMPLEX FORMED BETWEEN RUSSELL'S VIPER JRNL TITL 3 PHOSPHOLIPASE A2 AND A DESIGNED PEPTIDE LEU-ALA-ILE-TYR-SER JRNL TITL 4 (LAIYS). JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 1813 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 12351825 JRNL DOI 10.1107/S0907444902013720
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 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1312150.020 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 17841 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) : 0.187 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 861 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2684 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 143 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1928 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : -1.13000 REMARK 3 B33 (A**2) : 0.64000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.08 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.032 REMARK 3 BOND ANGLES (DEGREES) : 2.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.71 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) : 2.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.160 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.540 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.770 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 77.47 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 : CAR.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 : CAR.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 1JQ8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-AUG-01. REMARK 100 THE RCSB ID CODE IS RCSB014060.
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 : 17914 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 96.3 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.02000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.04300 REMARK 200 R SYM FOR SHELL (I) : 0.17000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.400 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: 1FE7 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 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 38.79500 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 38.79500 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 38.41250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.18750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.18750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.79500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.18750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.79500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.18750 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 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: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 355 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 531 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 331 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 333 LIES ON A SPECIAL POSITION.
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 SER P 5 C SER P 5 OXT 0.155 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 SER P 5 CB - CA - C ANGL. DEV. = 20.4 DEGREES REMARK 500 SER P 5 N - CA - CB ANGL. DEV. = -13.0 DEGREES REMARK 500 SER P 5 CA - CB - OG ANGL. DEV. = -18.3 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 SER A 24 24.73 -141.53 REMARK 500 GLU A 85 -167.88 -66.24 REMARK 500 LEU B 55 62.79 -117.78 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 487 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH A 526 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH B 376 DISTANCE = 5.69 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 303 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 REMARK 900 PULCHELLA AT 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: 1JQ9 RELATED DB: PDB REMARK 900 STRUCTURE OF DPLA2 COMPLEXED WITH PENTAPEPTIDE FLSYK
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COMPLETE SEQUENCE FOR THIS STRUCTURE REMARK 999 IS 121 RESIDUES LONG. GENBANK AAB47213 REMARK 999 (ACCESSION 1839639) MATCHED EXACTLY REMARK 999 WITH THE FIRST 50 RESIDUES OF THIS STRUCTURE. REMARK 999 AN ADEQUATE DATABASE MATCH COULD NOT BE REMARK 999 FOUND FOR THE COMPLETE 121 RESIDUE SEQUENCE. REMARK 999 THE COMPLETE SEQUENCE IS PRESENT IN THE REFERENCE REMARK 999 PAPER: GOWDA ET AL., TOXICON 32 (6) 665-673 (1994).
DBREF 1JQ8 A 1 133 PDB 1JQ8 1JQ8 1 133 DBREF 1JQ8 B 1 133 PDB 1JQ8 1JQ8 1 133 DBREF 1JQ8 P 1 5 PDB 1JQ8 1JQ8 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 LEU ALA ILE TYR SER
HET SO4 A 401 5 HET ACY A 301 4 HET ACY B 302 4 HET ACY B 303 4
HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID
FORMUL 4 SO4 O4 S 2- FORMUL 5 ACY 3(C2 H4 O2) FORMUL 8 HOH *283(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 ASN A 54 1 16 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 2.04 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 2.04 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 0.27 CISPEP 2 ILE B 19 PRO B 20 0 0.70
SITE 1 AC1 3 LYS A 131 CYS A 133 LYS B 69 SITE 1 AC2 4 LYS A 38 TYR A 120 HOH A 523 HOH B 318 SITE 1 AC3 3 ARG B 107 HOH B 366 HOH B 437 SITE 1 AC4 1 SER B 90 SITE 1 AC5 22 LEU A 2 LEU A 3 PHE A 5 GLY A 6 SITE 2 AC5 22 LYS A 7 LEU A 10 ALA A 18 ILE A 19 SITE 3 AC5 22 TYR A 22 TYR A 28 CYS A 29 GLY A 30 SITE 4 AC5 22 TRP A 31 CYS A 45 HIS A 48 ASP A 49 SITE 5 AC5 22 HOH A 504 HOH A 513 VAL B 47 ASN B 54 SITE 6 AC5 22 CYS B 133 HOH P 216
CRYST1 76.825 90.375 77.590 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 0.013017 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011065 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012888 0.00000