10 20 30 40 50 60 70 80 1JQ9 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 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) : -0.03 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) : 2.00 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.40 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 RCSB ID CODE IS RCSB014061.
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 <I/SIGMA(I)> 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) : 0.04700 REMARK 200 R SYM FOR SHELL (I) : 0.09000 REMARK 200 <I/SIGMA(I)> 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 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 398 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH A 401 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH B 375 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 388 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH B 437 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH B 438 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH B 439 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH B 448 DISTANCE = 5.31 ANGSTROMS
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 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: 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 B 303 4 HET ACY A 304 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