HEADER CARBOXYLIC ESTER HYDROLASE 27-JUN-83 3BP2 TITLE ROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC PHOSPHOLIPASE TITLE 2 A2 WITH AGGREGATED SUBSTRATES. PROPERTIES AND CRYSTAL STRUCTURE OF TITLE 3 TRANSAMINATED PHOSPHOLIPASE A2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS CARBOXYLIC ESTER HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.W.DIJKSTRA,J.DRENTH REVDAT 10 20-NOV-24 3BP2 1 REMARK REVDAT 9 15-NOV-23 3BP2 1 REMARK LINK ATOM REVDAT 8 20-NOV-19 3BP2 1 LINK REVDAT 7 29-NOV-17 3BP2 1 REMARK HELIX REVDAT 6 24-FEB-09 3BP2 1 VERSN REVDAT 5 01-APR-03 3BP2 1 JRNL REVDAT 4 15-JAN-91 3BP2 3 SEQRES HET FORMUL HETATM REVDAT 3 09-APR-85 3BP2 1 JRNL REVDAT 2 30-SEP-83 3BP2 1 REVDAT REVDAT 1 15-SEP-83 3BP2 0 JRNL AUTH B.W.DIJKSTRA,K.H.KALK,J.DRENTH,G.H.DE HAAS,M.R.EGMOND, JRNL AUTH 2 A.J.SLOTBOOM JRNL TITL ROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC JRNL TITL 2 PHOSPHOLIPASE A2 WITH AGGREGATED SUBSTRATES. PROPERTIES AND JRNL TITL 3 CRYSTAL STRUCTURE OF TRANSAMINATED PHOSPHOLIPASE A2 JRNL REF BIOCHEMISTRY V. 23 2759 1984 JRNL REFN ISSN 0006-2960 JRNL PMID 6466614 JRNL DOI 10.1021/BI00307A035 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.W.DIJKSTRA,R.RENETSEDER,K.H.KALK,W.G.J.HOL,J.DRENTH REMARK 1 TITL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 AT 2.6 REMARK 1 TITL 2 ANGSTROMS RESOLUTION AND COMPARISON WITH BOVINE REMARK 1 TITL 3 PHOSPHOLIPASE A2 REMARK 1 REF J.MOL.BIOL. V. 168 163 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.W.DIJKSTRA,G.J.H.VANNES,K.H.KALK,N.P.BRANDENBURG, REMARK 1 AUTH 2 W.G.J.HOL,J.DRENTH REMARK 1 TITL THE STRUCTURE OF BOVINE PANCREATIC PROPHOSPHOLIPASE A2 AT REMARK 1 TITL 2 3.0 ANGSTROMS RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 38 793 1982 REMARK 1 REFN ISSN 0108-7681 REMARK 1 REFERENCE 3 REMARK 1 AUTH B.W.DIJKSTRA,J.DRENTH,K.H.KALK REMARK 1 TITL ACTIVE SITE AND CATALYTIC MECHANISM OF PHOSPHOLIPASE A2 REMARK 1 REF NATURE V. 289 604 1981 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH B.W.DIJKSTRA,K.H.KALK,W.G.J.HOL,J.DRENTH REMARK 1 TITL STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE A2 AT 1.7 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 147 97 1981 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 5 REMARK 1 AUTH B.W.DIJKSTRA,J.DRENTH,K.H.KALK,P.J.VANDERMAELEN REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE AND DISULFIDE BOND CONNECTIONS REMARK 1 TITL 2 IN BOVINE PANCREATIC PHOSPHOLIPASE A2 REMARK 1 REF J.MOL.BIOL. V. 124 53 1978 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 23.34000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.95500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 18.95500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.34000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 400 REMARK 400 COMPOUND REMARK 400 THE TYPE CLASSIFICATIONS GIVEN IN THE REMARK FIELD OF THE REMARK 400 TURN RECORDS BELOW FOLLOWS THE NOMENCLATURE OF CRAWFORD ET REMARK 400 AL. (PROC.NAT.ACAD.SCI.USA, V. 76, P. 2551, 1973). REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 PYR A 1 REMARK 475 LEU A 2 REMARK 475 LYS A 53 REMARK 475 GLN A 54 REMARK 475 ALA A 55 REMARK 475 LYS A 56 REMARK 475 LYS A 57 REMARK 475 LEU A 58 REMARK 475 ASP A 59 REMARK 475 SER A 60 REMARK 475 CYS A 61 REMARK 475 LYS A 62 REMARK 475 VAL A 63 REMARK 475 LEU A 64 REMARK 475 VAL A 65 REMARK 475 ASP A 66 REMARK 475 ASN A 67 REMARK 475 PRO A 68 REMARK 475 TYR A 69 REMARK 475 THR A 70 REMARK 475 ASN A 71 REMARK 475 ASN A 72 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TRP A 3 O CB CG CD1 CD2 NE1 CE2 REMARK 480 TRP A 3 CE3 CZ2 CZ3 CH2 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 OD1 ASP A 66 O HOH A 162 0.43 REMARK 500 N TYR A 69 O HOH A 202 0.61 REMARK 500 CB PRO A 68 O HOH A 205 0.75 REMARK 500 C ASN A 71 O HOH A 197 0.82 REMARK 500 NE1 TRP A 3 O HOH A 206 0.83 REMARK 500 CA ASN A 71 O HOH A 197 0.92 REMARK 500 CG ASP A 66 O HOH A 162 0.98 REMARK 500 OG1 THR A 70 O HOH A 164 1.03 REMARK 500 CD1 LEU A 64 O HOH A 195 1.11 REMARK 500 C PRO A 68 O HOH A 202 1.11 REMARK 500 CA PRO A 68 O HOH A 205 1.13 REMARK 500 O TYR A 69 O HOH A 148 1.38 REMARK 500 CA TYR A 69 O HOH A 202 1.39 REMARK 500 CB THR A 70 O HOH A 164 1.44 REMARK 500 CG PRO A 68 O HOH A 205 1.44 REMARK 500 CE2 TRP A 3 O HOH A 206 1.59 REMARK 500 N ASN A 72 O HOH A 197 1.61 REMARK 500 CD1 TRP A 3 O HOH A 206 1.62 REMARK 500 N PRO A 68 O HOH A 205 1.65 REMARK 500 O PRO A 68 O HOH A 202 1.82 REMARK 500 CD PRO A 68 O HOH A 205 1.84 REMARK 500 CB ASN A 71 O HOH A 197 1.90 REMARK 500 O ASN A 71 O HOH A 197 1.91 REMARK 500 CG LEU A 64 O HOH A 195 1.98 REMARK 500 CB ASP A 66 O HOH A 162 1.99 REMARK 500 CG2 THR A 70 O HOH A 164 2.06 REMARK 500 OD2 ASP A 66 O HOH A 162 2.11 REMARK 500 OE2 GLU A 92 O HOH A 156 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 114 O HOH A 169 2554 2.05 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 TRP A 3 CB TRP A 3 CG 0.300 REMARK 500 GLY A 35 N GLY A 35 CA 0.099 REMARK 500 LEU A 64 N LEU A 64 CA -0.226 REMARK 500 ASN A 72 C TYR A 73 N 0.264 REMARK 500 SER A 74 CB SER A 74 OG 0.079 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 PYR A 1 CA - C - N ANGL. DEV. = 38.8 DEGREES REMARK 500 PYR A 1 O - C - N ANGL. DEV. = -54.2 DEGREES REMARK 500 TRP A 3 CA - CB - CG ANGL. DEV. = 11.9 DEGREES REMARK 500 GLN A 4 N - CA - CB ANGL. DEV. = 12.7 DEGREES REMARK 500 ASP A 21 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 ASP A 40 CB - CG - OD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG A 43 CD - NE - CZ ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 43 NE - CZ - NH2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 CYS A 51 CB - CA - C ANGL. DEV. = 7.9 DEGREES REMARK 500 TYR A 52 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 52 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 LEU A 58 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 LEU A 64 N - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 ASN A 72 CA - C - N ANGL. DEV. = 14.2 DEGREES REMARK 500 ASN A 72 O - C - N ANGL. DEV. = -16.9 DEGREES REMARK 500 GLU A 92 OE1 - CD - OE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 PHE A 94 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 100 CD - NE - CZ ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG A 100 NH1 - CZ - NH2 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 100 NE - CZ - NH2 ANGL. DEV. = -9.6 DEGREES REMARK 500 CYS A 105 CB - CA - C ANGL. DEV. = 9.9 DEGREES REMARK 500 ASP A 119 CA - CB - CG ANGL. DEV. = -14.0 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 LEU A 2 -57.59 68.64 REMARK 500 LYS A 62 61.29 -63.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 43 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PYR A 1 -67.28 REMARK 500 ASN A 72 -13.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 124 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 28 O REMARK 620 2 GLY A 30 O 87.4 REMARK 620 3 GLY A 32 O 90.3 77.4 REMARK 620 4 ASP A 49 OD1 114.9 138.4 133.1 REMARK 620 5 ASP A 49 OD2 104.1 157.7 83.4 53.4 REMARK 620 6 HOH A 126 O 88.4 71.4 148.8 74.5 127.0 REMARK 620 7 HOH A 133 O 165.4 78.0 86.3 77.2 89.6 87.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 124 DBREF 3BP2 A 2 123 UNP P00593 PA21B_BOVIN 24 145 SEQRES 1 A 123 PYR LEU TRP GLN PHE ASN GLY MET ILE LYS CYS LYS ILE SEQRES 2 A 123 PRO SER SER GLU PRO LEU LEU ASP PHE ASN ASN TYR GLY SEQRES 3 A 123 CYS TYR CYS GLY LEU GLY GLY SER GLY THR PRO VAL ASP SEQRES 4 A 123 ASP LEU ASP ARG CYS CYS GLN THR HIS ASP ASN CYS TYR SEQRES 5 A 123 LYS GLN ALA LYS LYS LEU ASP SER CYS LYS VAL LEU VAL SEQRES 6 A 123 ASP ASN PRO TYR THR ASN ASN TYR SER TYR SER CYS SER SEQRES 7 A 123 ASN ASN GLU ILE THR CYS SER SER GLU ASN ASN ALA CYS SEQRES 8 A 123 GLU ALA PHE ILE CYS ASN CYS ASP ARG ASN ALA ALA ILE SEQRES 9 A 123 CYS PHE SER LYS VAL PRO TYR ASN LYS GLU HIS LYS ASN SEQRES 10 A 123 LEU ASP LYS LYS ASN CYS HET PYR A 1 5 HET CA A 124 1 HETNAM PYR PYRUVIC ACID HETNAM CA CALCIUM ION FORMUL 1 PYR C3 H4 O3 FORMUL 2 CA CA 2+ FORMUL 3 HOH *86(H2 O) HELIX 1 A TRP A 3 ILE A 13 1 11 HELIX 2 B GLU A 17 PHE A 22 1GLU17 ALSO CLASS 5 WITH LEU20 6 HELIX 3 C ASP A 39 LEU A 58 1GLN 54, ALA 55 CLASS 5 20 HELIX 4 E ASN A 89 LYS A 108 1CYS 105 CLASS 5 20 SHEET 1 SH1 2 SER A 74 SER A 78 0 SHEET 2 SH1 2 GLU A 81 SER A 85 -1 SSBOND 1 CYS A 11 CYS A 77 1555 1555 2.12 SSBOND 2 CYS A 27 CYS A 123 1555 1555 2.02 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.05 SSBOND 4 CYS A 44 CYS A 105 1555 1555 2.02 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.05 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.08 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.05 LINK C PYR A 1 N LEU A 2 1555 1555 1.41 LINK O PYR A 1 N LEU A 2 1555 1555 1.48 LINK CA PYR A 1 CG ASP A 59 1555 4457 1.28 LINK CB PYR A 1 CG ASP A 59 1555 4457 1.20 LINK O TYR A 28 CA CA A 124 1555 1555 2.10 LINK O GLY A 30 CA CA A 124 1555 1555 2.50 LINK O GLY A 32 CA CA A 124 1555 1555 2.42 LINK OD1 ASP A 49 CA CA A 124 1555 1555 2.34 LINK OD2 ASP A 49 CA CA A 124 1555 1555 2.25 LINK CA CA A 124 O HOH A 126 1555 1555 2.52 LINK CA CA A 124 O HOH A 133 1555 1555 2.45 SITE 1 AC1 6 TYR A 28 GLY A 30 GLY A 32 ASP A 49 SITE 2 AC1 6 HOH A 126 HOH A 133 CRYST1 46.680 64.850 37.910 90.00 90.00 90.00 P 21 21 21 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 0.021422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026378 0.00000 HETATM 1 C PYR A 1 9.426 15.847 31.750 0.00 19.40 C HETATM 2 O PYR A 1 9.457 14.648 31.631 0.00 19.44 O HETATM 3 CA PYR A 1 8.841 16.344 33.063 0.00 19.09 C HETATM 4 O3 PYR A 1 7.918 17.344 33.608 0.00 18.97 O HETATM 5 CB PYR A 1 8.168 14.955 33.043 0.00 18.93 C