10 20 30 40 50 60 70 80 1KPM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 01-JAN-02 1KPM
TITLE FIRST STRUCTURAL EVIDENCE OF A SPECIFIC INHIBITION OF PHOSPHOLIPASE A2 TITLE 2 BY VITAMIN E AND ITS IMPLICATIONS IN INFLAMMATION: CRYSTAL STRUCTURE TITLE 3 OF THE COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND VITAMIN E AT 1.8 A TITLE 4 RESOLUTION.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.1.4
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DABOIA RUSSELLII PULCHELLA; SOURCE 3 ORGANISM_TAXID: 97228; SOURCE 4 STRAIN: PULCHELLA; SOURCE 5 SECRETION: VENOM
KEYWDS PHOSPHOLIPASE A2, DABOIA RUSSELLI PULCHELLA, NEUROTOXIC, KEYWDS 2 INFLAMMATION, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.CHANDRA,J.JASTI,P.KAUR,C.BETZEL,A.SRINIVASAN,T.P.SINGH
REVDAT 3 16-NOV-11 1KPM 1 VERSN HETATM REVDAT 2 24-FEB-09 1KPM 1 VERSN REVDAT 1 10-JUL-02 1KPM 0
SPRSDE 10-JUL-02 1KPM 1FE7
JRNL AUTH V.CHANDRA,J.JASTI,P.KAUR,C.BETZEL,A.SRINIVASAN,T.P.SINGH JRNL TITL FIRST STRUCTURAL EVIDENCE OF A SPECIFIC INHIBITION OF JRNL TITL 2 PHOSPHOLIPASE A2 BY ALPHA-TOCOPHEROL (VITAMIN E) AND ITS JRNL TITL 3 IMPLICATIONS IN INFLAMMATION: CRYSTAL STRUCTURE OF THE JRNL TITL 4 COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ALPHA-TOCOPHEROL JRNL TITL 5 AT 1.8 A RESOLUTION JRNL REF J.MOL.BIOL. V. 320 215 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12079380 JRNL DOI 10.1016/S0022-2836(02)00473-4
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.CHANDRA,J.JASTI,P.KAUR,C.BETZEL,A.SRINIVASAN,T.P.SINGH REMARK 1 TITL FIRST STRUCTURAL EVIDENCE OF ANTIINFLAMMATORY ACTION OF REMARK 1 TITL 2 VITAMIN E (2,5,7,8-TETRAMETHYL-2-(4',8',12'- REMARK 1 TITL 3 TRIMETHYLTRIDECYL)-6-CHROMANOL) THROUGH ITS BINDING TO REMARK 1 TITL 4 PHOSPHOLIPASE A2 SPECIFICALLY: CRYSTAL STRUCTURE OF A REMARK 1 TITL 5 COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND VITAMIN E AT REMARK 1 TITL 6 1.80 RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH V.CHANDRA,J.JASTI,P.KAUR,C.BETZEL,A.SRINIVASAN,T.P.SINGH REMARK 1 TITL CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE REMARK 1 TITL 2 A2 FROM DABOIA RUSSELLI PULCHELLA AND A DESIGNED REMARK 1 TITL 3 PENTAPEPTIDE PHE-LEU-SER-TYR-LYS AT 1.8 RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN 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 THE INHIBITION OF PHOSPHOLIPASE REMARK 1 TITL 2 A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX REMARK 1 TITL 3 FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 4 REMARK 1 AUTH V.CHANDRA,J.JASTI,P.KAUR,C.BETZEL,A.SRINIVASAN,T.P.SINGH REMARK 1 TITL DESIGN OF SPECIFIC INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL REMARK 1 TITL 2 STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 FROM REMARK 1 TITL 3 DABOIA RUSSELLI PULCHELLA AND A DESIGNED PENTAPEPTIDE REMARK 1 TITL 4 LEU-ALA-ILE-TYR-SER AT 2.0 RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 5 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 6 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 A 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 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 23652 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) : 0.197 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1139 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) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3803 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 189 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1888 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 306 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.024 REMARK 3 BOND ANGLES (DEGREES) : 2.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 4.01 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) : 0.900 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.500 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.360 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.100 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 70.68 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : VIT.PARAM REMARK 3 PARAMETER FILE 5 : PAR.PARAM REMARK 3 PARAMETER FILE 6 : 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 : VIT.TOP REMARK 3 TOPOLOGY FILE 5 : TOP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE
REMARK 4 REMARK 4 1KPM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-02. REMARK 100 THE RCSB ID CODE IS RCSB015202.
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) : 180.0 REMARK 200 PH : 6.50 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 : MIRRORS 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 : 23652 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.03800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9300 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18500 REMARK 200 R SYM FOR SHELL (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: 1CL5 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM SODIUM CACODYLATE, 1.4M AMMONIUM REMARK 280 SULFATE, 4MM CALCIUM CHLORIDE, 3% DIOXANE, PH 6.50, 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 39.02000 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 39.02000 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 37.89500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.25500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.89500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.25500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.02000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.89500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.25500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.02000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.89500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.25500 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 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 THE INHIBITOR VITAMIN E
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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 A 596 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 598 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 577 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 658 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 589 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 TRP A 31 CA TRP A 31 CB -0.330 REMARK 500 GLY A 30 C TRP A 31 N -0.174 REMARK 500 LYS A 127 CG LYS A 127 CD -0.229 REMARK 500 LYS A 127 CD LYS A 127 CE -0.244 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 TRP A 31 CB - CA - C ANGL. DEV. = 22.5 DEGREES REMARK 500 TRP A 31 N - CA - CB ANGL. DEV. = -18.3 DEGREES REMARK 500 TRP A 31 CA - CB - CG ANGL. DEV. = 41.1 DEGREES REMARK 500 LYS A 127 CB - CG - CD ANGL. DEV. = -23.0 DEGREES REMARK 500 LYS A 127 CG - CD - CE ANGL. DEV. = 49.1 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 19.47 -147.18 REMARK 500 ASP A 39 -168.99 -163.17 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 608 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A 614 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH A 620 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH A 629 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH A 631 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 632 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 636 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 643 DISTANCE = 7.06 ANGSTROMS REMARK 525 HOH B 624 DISTANCE = 5.50 ANGSTROMS REMARK 525 HOH B 637 DISTANCE = 5.48 ANGSTROMS REMARK 525 HOH B 644 DISTANCE = 7.76 ANGSTROMS REMARK 525 HOH B 649 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH B 657 DISTANCE = 8.34 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VIT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 504
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FE7 RELATED DB: PDB REMARK 900 1FE7 IS THE STRUCTURE OF DPLA2 COMPLEXED WITH VITAMIN E REMARK 900 RELATED ID: 1FB2 RELATED DB: PDB REMARK 900 1FB2 IS THE STRUCTURE OF DPLA2 AT 1.95 REMARK 900 RELATED ID: 1CL5 RELATED DB: PDB REMARK 900 1CL5 IS THE STRUCTURE OF DPLA2 AT 2.45 REMARK 900 RELATED ID: 1JQ8 RELATED DB: PDB REMARK 900 1JQ8 IS THE STRUCTURE OF DPLA2 COMPLEXED WITH PENTAPEPTIDE REMARK 900 LAIYS REMARK 900 RELATED ID: 1JQ9 RELATED DB: PDB REMARK 900 1JQ9 IS THE STRUCTURE OF DPLA2 COMPLEXED WITH PENTAPEPTIDE REMARK 900 FLSYK REMARK 900 RELATED ID: 1FV0 RELATED DB: PDB REMARK 900 1FV0 IS THE STRUCTURE OF DPLA2 COMPLEXED WITH ARISTOLOCHIC REMARK 900 ACID
DBREF 1KPM A 1 51 UNP P59071 PA28_DABRP 1 50 DBREF 1KPM B 1 51 UNP P59071 PA28_DABRP 1 50
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
HET VIT A 401 31 HET ACY B 501 4 HET ACY B 502 4 HET ACY B 503 4 HET ACY A 504 4
HETNAM VIT VITAMIN E HETNAM ACY ACETIC ACID
HETSYN VIT 2,5,7,8-TETRAMETHYL-2-(4,8,12-TRIMETHYLTRIDECYL)-6- HETSYN 2 VIT CHROMANOL
FORMUL 3 VIT C29 H50 O2 FORMUL 4 ACY 4(C2 H4 O2) FORMUL 8 HOH *306(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 MET B 118 5 5 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 VAL A 83 N LYS A 76 SHEET 1 B 2 TYR B 75 VAL B 78 0 SHEET 2 B 2 ALA B 81 CYS B 84 -1 O VAL B 83 N LYS B 76
SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.02 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 2.02 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 0.69 CISPEP 2 ILE B 19 PRO B 20 0 0.63
SITE 1 AC1 17 LEU A 2 LEU A 3 GLY A 6 LYS A 7 SITE 2 AC1 17 ALA A 18 ILE A 19 TYR A 22 SER A 23 SITE 3 AC1 17 TYR A 28 CYS A 45 HIS A 48 ASP A 49 SITE 4 AC1 17 LYS A 69 HOH A 508 HOH A 517 ASN B 54 SITE 5 AC1 17 CYS B 133 SITE 1 AC2 4 PRO A 121 GLU B 11 ARG B 77 ARG B 107 SITE 1 AC3 5 PRO A 121 PHE A 124 ARG B 107 GLN B 108 SITE 2 AC3 5 HOH B 540 SITE 1 AC4 3 THR B 89 SER B 90 HOH B 596 SITE 1 AC5 3 ARG A 43 HOH A 537 HOH A 641
CRYST1 75.790 88.510 78.040 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 0.013194 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011298 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012814 0.00000