HEADER HYDROLASE 11-AUG-99 1CQR TITLE CRYSTAL STRUCTURE OF THE STROMELYSIN CATALYTIC DOMAIN AT 2.0 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMELYSIN-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HUMAN MATRIX METALLOPROTEINASE-3; COMPND 5 EC: 3.4.24.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACTIVE, TRUNCATED NATIVE ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.CHEN,T.J.RYDEL,F.GU,C.M.DUNAWAY,S.PIKUL,K.M.DUNHAM,B.L.BARNETT REVDAT 4 13-JUL-11 1CQR 1 VERSN REVDAT 3 24-FEB-09 1CQR 1 VERSN REVDAT 2 01-APR-03 1CQR 1 JRNL REVDAT 1 20-MAR-00 1CQR 0 JRNL AUTH L.CHEN,T.J.RYDEL,F.GU,C.M.DUNAWAY,S.PIKUL,K.M.DUNHAM, JRNL AUTH 2 B.L.BARNETT JRNL TITL CRYSTAL STRUCTURE OF THE STROMELYSIN CATALYTIC DOMAIN AT 2.0 JRNL TITL 2 A RESOLUTION: INHIBITOR-INDUCED CONFORMATIONAL CHANGES. JRNL REF J.MOL.BIOL. V. 293 545 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10543949 JRNL DOI 10.1006/JMBI.1999.3147 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.PIKUL,K.L.MCDOW DUNHAM,N.G.ALMSTEAD,B.DE,M.G.NATCHUS, REMARK 1 AUTH 2 M.V.ANASTASIO,S.J.MCPHAIL,C.E.SNIDER,Y.O.TAIWO,L.CHEN, REMARK 1 AUTH 3 C.M.DUNAWAY,F.GU,G.E.MIELING REMARK 1 TITL DESIGN AND SYNTHESIS OF PHOSPHINAMIDE-BASED HYDROXAMIC ACIDS REMARK 1 TITL 2 AS INHIBITORS OF MATRIX METALLOPROTEINASES REMARK 1 REF J.MED.CHEM. V. 42 87 1999 REMARK 1 REFN ISSN 0022-2623 REMARK 1 DOI 10.1021/JM980142S REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 21471 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) : 0.199 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2147 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2722 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.70 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 3.21 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB009496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-96 REMARK 200 TEMPERATURE (KELVIN) : 298. REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21471 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 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) : 12.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.05800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-24% PEG 8000, 2.5% 2-PROPANOL, 10MM REMARK 280 CACL2, 0.1 M TRIS-HCL BUFFER, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.K 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 19.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.70000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.70000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.55000 REMARK 290 SMTRY3 4 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 BIOLOGICAL ASSEMBLY IS A MONOMER 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -19.10000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 79.10000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -53.70000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 252 REMARK 465 PRO A 253 REMARK 465 GLU A 254 REMARK 465 THR A 255 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 HIS A 151 NE2 HIS A 151 CD2 -0.073 REMARK 500 HIS A 201 NE2 HIS A 201 CD2 -0.067 REMARK 500 HIS A 211 NE2 HIS A 211 CD2 -0.068 REMARK 500 HIS B 166 NE2 HIS B 166 CD2 -0.079 REMARK 500 HIS B 179 NE2 HIS B 179 CD2 -0.070 REMARK 500 HIS B 201 NE2 HIS B 201 CD2 -0.079 REMARK 500 ASP B 228 C LEU B 229 N -0.162 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 92 CD1 - CG - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP A 92 CE2 - CD2 - CG ANGL. DEV. = -6.5 DEGREES REMARK 500 TRP A 92 CG - CD2 - CE3 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 107 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 111 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 ASP A 111 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TRP A 124 CD1 - CG - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP A 124 CE2 - CD2 - CG ANGL. DEV. = -6.1 DEGREES REMARK 500 TRP A 124 CG - CD2 - CE3 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR A 168 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASP A 181 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP A 186 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP A 186 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 THR A 230 N - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 TRP B 92 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TRP B 92 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 93 CA - CB - CG ANGL. DEV. = 13.7 DEGREES REMARK 500 ARG B 100 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B 107 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP B 124 CD1 - CG - CD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP B 124 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP B 186 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP B 186 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 233 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 PHE B 232 CA - C - N ANGL. DEV. = -14.1 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 PHE A 86 164.39 -48.87 REMARK 500 ARG A 149 -125.89 49.65 REMARK 500 HIS A 151 11.14 -142.55 REMARK 500 ASN A 162 -110.61 54.45 REMARK 500 ASP A 189 -153.61 -118.68 REMARK 500 PHE A 210 -169.52 -105.06 REMARK 500 SER A 225 73.36 -111.82 REMARK 500 LEU A 229 17.39 -46.24 REMARK 500 ARG B 149 -120.12 42.61 REMARK 500 ASN B 162 -113.17 53.72 REMARK 500 ASP B 189 -150.85 -99.38 REMARK 500 SER B 225 51.36 -107.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 229 THR A 230 148.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 229 23.7 L L OUTSIDE RANGE REMARK 500 THR A 230 49.5 L L OUTSIDE RANGE REMARK 500 ASP B 228 24.2 L L OUTSIDE RANGE 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 ZN A1301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 205 NE2 REMARK 620 2 HIS A 211 NE2 104.0 REMARK 620 3 HIS A 201 NE2 97.4 108.6 REMARK 620 4 THR B 255 O 109.4 95.0 138.7 REMARK 620 5 THR B 255 OXT 113.1 135.5 90.5 50.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 153 OD2 REMARK 620 2 HIS A 166 NE2 108.9 REMARK 620 3 HIS A 151 NE2 108.3 121.1 REMARK 620 4 HIS A 179 ND1 97.9 109.2 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 159 O REMARK 620 2 GLY A 161 O 95.4 REMARK 620 3 ASP A 158 OD1 87.7 83.9 REMARK 620 4 VAL A 163 O 174.8 86.9 88.0 REMARK 620 5 ASP A 181 OD2 84.5 179.6 96.5 93.3 REMARK 620 6 GLU A 184 OE2 95.7 90.6 173.8 88.8 89.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 OD2 REMARK 620 2 ASP A 182 O 146.0 REMARK 620 3 GLU A 184 O 74.7 77.9 REMARK 620 4 ASP A 107 OD1 52.2 158.1 123.9 REMARK 620 5 ASP A 182 OD1 86.8 82.1 106.6 89.0 REMARK 620 6 HOH A 6 O 127.8 83.3 156.0 76.1 85.2 REMARK 620 7 HOH A 43 O 96.5 99.6 82.7 86.3 170.7 85.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 59 O REMARK 620 2 ASP A 177 OD1 98.4 REMARK 620 3 ASN A 175 O 167.0 93.9 REMARK 620 4 GLY A 173 O 82.9 98.8 91.0 REMARK 620 5 ASP A 141 O 92.6 83.1 93.1 175.3 REMARK 620 6 HOH A 33 O 96.7 160.7 72.3 95.0 84.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 201 NE2 REMARK 620 2 HOH B 61 O 112.6 REMARK 620 3 HIS B 211 NE2 105.5 124.7 REMARK 620 4 HIS B 205 NE2 95.6 115.1 98.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 179 ND1 REMARK 620 2 HIS B 166 NE2 101.5 REMARK 620 3 ASP B 153 OD2 98.0 110.8 REMARK 620 4 HIS B 151 NE2 112.2 122.4 109.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 159 O REMARK 620 2 GLY B 161 O 89.6 REMARK 620 3 VAL B 163 O 176.4 94.0 REMARK 620 4 ASP B 181 OD2 88.1 177.3 88.3 REMARK 620 5 GLU B 184 OE2 86.9 95.0 92.2 83.5 REMARK 620 6 ASP B 158 OD1 89.9 84.7 90.9 96.7 176.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 34 O REMARK 620 2 HOH B 62 O 77.7 REMARK 620 3 ASP B 107 OD1 80.4 78.1 REMARK 620 4 ASP B 107 OD2 133.3 92.4 52.9 REMARK 620 5 ASP B 182 O 75.7 105.0 154.6 149.5 REMARK 620 6 GLU B 184 O 148.2 85.5 122.4 73.6 83.0 REMARK 620 7 ASP B 182 OD1 94.0 170.6 96.4 90.2 76.7 104.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 141 O REMARK 620 2 GLY B 173 O 176.0 REMARK 620 3 ASN B 175 O 98.0 86.0 REMARK 620 4 HOH B 41 O 84.7 96.3 81.7 REMARK 620 5 ASP B 177 OD1 86.0 93.4 92.5 168.2 REMARK 620 6 HOH B 5 O 90.7 85.4 169.6 93.4 93.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BIW RELATED DB: PDB REMARK 900 DESIGN AND SYNTHESIS OF CONFORMATIONALLY-CONSTRAINED MMP REMARK 900 INHIBITORS REMARK 900 RELATED ID: 1B3D RELATED DB: PDB REMARK 900 DESIGN AND SYNTHESIS OF PHOSPHINAMIDE-BASED HYDROXAMIC REMARK 900 ACIDS AS INHIBITORS OF MMP REMARK 900 RELATED ID: 1BQO RELATED DB: PDB REMARK 900 DISCOVERY OF POTENT, ACHIRAL MATRIX METALLOPROTEINASE REMARK 900 INHIBITORS DBREF 1CQR A 83 255 UNP P08254 MMP3_HUMAN 100 272 DBREF 1CQR B 83 255 UNP P08254 MMP3_HUMAN 100 272 SEQRES 1 A 173 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 A 173 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 A 173 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 A 173 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 A 173 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 A 173 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 173 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 A 173 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 A 173 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 A 173 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 A 173 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 A 173 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 A 173 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 A 173 SER PRO GLU THR SEQRES 1 B 173 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 B 173 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 B 173 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 B 173 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 B 173 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 B 173 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 173 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 B 173 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 B 173 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 B 173 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 B 173 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 B 173 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 B 173 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 B 173 SER PRO GLU THR HET ZN A1301 1 HET ZN A1302 1 HET CA A1303 1 HET CA A1304 1 HET CA A1305 1 HET ZN B2301 1 HET ZN B2302 1 HET CA B2303 1 HET CA B2304 1 HET CA B2305 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 13 HOH *82(H2 O) HELIX 1 1 PRO A 109 GLU A 126 1 18 HELIX 2 2 LEU A 195 LEU A 207 1 13 HELIX 3 3 SER A 235 GLY A 247 1 13 HELIX 4 4 PRO B 109 GLU B 126 1 18 HELIX 5 5 LEU B 195 GLY B 208 1 14 HELIX 6 6 THR B 227 PHE B 232 1 6 HELIX 7 7 SER B 235 TYR B 246 1 12 SHEET 1 A 2 ARG A 84 THR A 85 0 SHEET 2 A 2 LEU A 209 PHE A 210 -1 N PHE A 210 O ARG A 84 SHEET 1 B 5 THR A 131 ARG A 134 0 SHEET 2 B 5 HIS A 96 ILE A 101 1 N LEU A 97 O THR A 131 SHEET 3 B 5 ILE A 142 ALA A 147 1 N ILE A 142 O THR A 98 SHEET 4 B 5 ALA A 178 ASP A 181 1 N ALA A 178 O MET A 143 SHEET 5 B 5 ALA A 165 ALA A 167 -1 O HIS A 166 N HIS A 179 SHEET 1 C 2 TRP A 186 THR A 187 0 SHEET 2 C 2 THR A 193 ASN A 194 1 O THR A 193 N THR A 187 SHEET 1 D 2 ARG B 84 THR B 85 0 SHEET 2 D 2 LEU B 209 PHE B 210 -1 N PHE B 210 O ARG B 84 SHEET 1 E 5 THR B 131 ARG B 134 0 SHEET 2 E 5 HIS B 96 ILE B 101 1 N LEU B 97 O THR B 131 SHEET 3 E 5 ILE B 142 ALA B 147 1 N ILE B 142 O THR B 98 SHEET 4 E 5 ALA B 178 ASP B 181 1 N ALA B 178 O MET B 143 SHEET 5 E 5 ALA B 165 ALA B 167 -1 O HIS B 166 N HIS B 179 SHEET 1 F 2 TRP B 186 THR B 187 0 SHEET 2 F 2 THR B 193 ASN B 194 1 O THR B 193 N THR B 187 LINK ZN ZN A1301 NE2 HIS A 205 1555 1555 2.19 LINK ZN ZN A1301 NE2 HIS A 211 1555 1555 2.18 LINK ZN ZN A1301 NE2 HIS A 201 1555 1555 2.15 LINK ZN ZN A1302 OD2 ASP A 153 1555 1555 2.09 LINK ZN ZN A1302 NE2 HIS A 166 1555 1555 2.13 LINK ZN ZN A1302 NE2 HIS A 151 1555 1555 2.10 LINK ZN ZN A1302 ND1 HIS A 179 1555 1555 2.10 LINK CA CA A1303 O GLY A 159 1555 1555 2.29 LINK CA CA A1303 O GLY A 161 1555 1555 2.36 LINK CA CA A1303 OD1 ASP A 158 1555 1555 2.33 LINK CA CA A1303 O VAL A 163 1555 1555 2.32 LINK CA CA A1303 OD2 ASP A 181 1555 1555 2.26 LINK CA CA A1303 OE2 GLU A 184 1555 1555 2.27 LINK CA CA A1304 OD2 ASP A 107 1555 1555 2.35 LINK CA CA A1304 O ASP A 182 1555 1555 2.36 LINK CA CA A1304 O GLU A 184 1555 1555 2.37 LINK CA CA A1304 OD1 ASP A 107 1555 1555 2.37 LINK CA CA A1304 OD1 ASP A 182 1555 1555 2.36 LINK CA CA A1304 O HOH A 6 1555 1555 2.44 LINK CA CA A1304 O HOH A 43 1555 1555 2.38 LINK CA CA A1305 O HOH A 59 1555 1555 2.35 LINK CA CA A1305 OD1 ASP A 177 1555 1555 2.29 LINK CA CA A1305 O ASN A 175 1555 1555 2.37 LINK CA CA A1305 O GLY A 173 1555 1555 2.31 LINK CA CA A1305 O ASP A 141 1555 1555 2.34 LINK CA CA A1305 O HOH A 33 1555 1555 2.42 LINK ZN ZN B2301 NE2 HIS B 201 1555 1555 2.15 LINK ZN ZN B2301 O HOH B 61 1555 1555 2.03 LINK ZN ZN B2301 NE2 HIS B 211 1555 1555 2.19 LINK ZN ZN B2301 NE2 HIS B 205 1555 1555 2.18 LINK ZN ZN B2302 ND1 HIS B 179 1555 1555 2.13 LINK ZN ZN B2302 NE2 HIS B 166 1555 1555 2.11 LINK ZN ZN B2302 OD2 ASP B 153 1555 1555 2.05 LINK ZN ZN B2302 NE2 HIS B 151 1555 1555 2.14 LINK CA CA B2303 O GLY B 159 1555 1555 2.27 LINK CA CA B2303 O GLY B 161 1555 1555 2.32 LINK CA CA B2303 O VAL B 163 1555 1555 2.27 LINK CA CA B2303 OD2 ASP B 181 1555 1555 2.28 LINK CA CA B2303 OE2 GLU B 184 1555 1555 2.31 LINK CA CA B2303 OD1 ASP B 158 1555 1555 2.30 LINK CA CA B2304 O HOH B 34 1555 1555 2.43 LINK CA CA B2304 O HOH B 62 1555 1555 2.41 LINK CA CA B2304 OD1 ASP B 107 1555 1555 2.38 LINK CA CA B2304 OD2 ASP B 107 1555 1555 2.34 LINK CA CA B2304 O ASP B 182 1555 1555 2.36 LINK CA CA B2304 O GLU B 184 1555 1555 2.35 LINK CA CA B2304 OD1 ASP B 182 1555 1555 2.36 LINK CA CA B2305 O ASP B 141 1555 1555 2.33 LINK CA CA B2305 O GLY B 173 1555 1555 2.30 LINK CA CA B2305 O ASN B 175 1555 1555 2.30 LINK CA CA B2305 O HOH B 41 1555 1555 2.35 LINK CA CA B2305 OD1 ASP B 177 1555 1555 2.33 LINK CA CA B2305 O HOH B 5 1555 1555 2.37 LINK ZN ZN A1301 O THR B 255 1555 2464 1.72 LINK ZN ZN A1301 OXT THR B 255 1555 2464 2.70 SITE 1 AC1 4 HIS A 201 HIS A 205 HIS A 211 THR B 255 SITE 1 AC2 4 HIS A 151 ASP A 153 HIS A 166 HIS A 179 SITE 1 AC3 6 ASP A 158 GLY A 159 GLY A 161 VAL A 163 SITE 2 AC3 6 ASP A 181 GLU A 184 SITE 1 AC4 5 HOH A 6 HOH A 43 ASP A 107 ASP A 182 SITE 2 AC4 5 GLU A 184 SITE 1 AC5 6 HOH A 33 HOH A 59 ASP A 141 GLY A 173 SITE 2 AC5 6 ASN A 175 ASP A 177 SITE 1 AC6 4 HOH B 61 HIS B 201 HIS B 205 HIS B 211 SITE 1 AC7 4 HIS B 151 ASP B 153 HIS B 166 HIS B 179 SITE 1 AC8 6 ASP B 158 GLY B 159 GLY B 161 VAL B 163 SITE 2 AC8 6 ASP B 181 GLU B 184 SITE 1 AC9 5 HOH B 34 HOH B 62 ASP B 107 ASP B 182 SITE 2 AC9 5 GLU B 184 SITE 1 BC1 6 HOH B 5 HOH B 41 ASP B 141 GLY B 173 SITE 2 BC1 6 ASN B 175 ASP B 177 CRYST1 38.200 79.100 107.400 90.00 90.00 90.00 P 21 21 21 8 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 0.026178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012642 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009311 0.00000 MASTER 542 0 10 7 18 0 16 6 0 0 0 28 END