HEADER HYDROLASE 02-JUL-08 3DNG TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN MMP-8 AND A NON-ZINC TITLE 2 CHELATING INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL COLLAGENASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MMP-8 CATALYTIC DOMAIN, UNP RESIDUES 100-262; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-8, MMP-8, PMNL COLLAGENASE, PMNL- COMPND 6 CL; COMPND 7 EC: 3.4.24.34; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP8, CLG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSVB30 KEYWDS HYDROLASE, SELECTIVE INHIBITION, NON-ZINC CHELATING INHIBITORS, KEYWDS 2 CALCIUM, COLLAGEN DEGRADATION, EXTRACELLULAR MATRIX, GLYCOPROTEIN, KEYWDS 3 METAL-BINDING, METALLOPROTEASE, POLYMORPHISM, PROTEASE, SECRETED, KEYWDS 4 ZINC, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR G.POCHETTI,R.MONTANARI,F.MAZZA REVDAT 3 01-NOV-23 3DNG 1 REMARK REVDAT 2 13-DEC-17 3DNG 1 REMARK REVDAT 1 03-MAR-09 3DNG 0 JRNL AUTH G.POCHETTI,R.MONTANARI,C.GEGE,C.CHEVRIER,A.G.TAVERAS,F.MAZZA JRNL TITL EXTRA BINDING REGION INDUCED BY NON-ZINC CHELATING JRNL TITL 2 INHIBITORS INTO THE S(1)' SUBSITE OF MATRIX JRNL TITL 3 METALLOPROTEINASE 8 (MMP-8) JRNL REF J.MED.CHEM. V. 52 1040 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19173605 JRNL DOI 10.1021/JM801166J REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.K.ENGEL,B.PIRARD,S.SCHIMANSKI,R.KIRSCH,J.HABERMANN, REMARK 1 AUTH 2 O.KLINGLER,V.SCHLOTTE,K.U.WEITHMANN,K.U.WENDT REMARK 1 TITL STRUCTURAL BASIS FOR THE HIGHLY SELECTIVE INHIBITION OF REMARK 1 TITL 2 MMP-13 REMARK 1 REF CHEM.BIOL. V. 12 181 2005 REMARK 1 REFN ISSN 1074-5521 REMARK 1 PMID 15734640 REMARK 1 DOI 10.1016/J.CHEMBIOL.2004.11.014 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.R.JOHNSON,A.G.PAVLOVSKY,D.F.ORTWINE,F.PRIOR,C.F.MAN, REMARK 1 AUTH 2 D.A.BORNEMEIER,C.A.BANOTAI,W.T.MUELLER,P.MCCONNELL,C.YAN, REMARK 1 AUTH 3 V.BARAGI,C.LESCH,W.H.ROARK,M.WILSON,K.DATTA,R.GUZMAN, REMARK 1 AUTH 4 H.K.HAN,R.D.DYER REMARK 1 TITL DISCOVERY AND CHARACTERIZATION OF A NOVEL INHIBITOR OF REMARK 1 TITL 2 MATRIX METALLOPROTEASE-13 THAT REDUCES CARTILAGE DAMAGE IN REMARK 1 TITL 3 VIVO WITHOUT JOINT FIBROPLASIA SIDE EFFECTS REMARK 1 REF J.BIOL.CHEM. V. 282 27781 2007 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 17623656 REMARK 1 DOI 10.1074/JBC.M703286200 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.MORALES,S.PERRIER,J.M.FLORENT,J.BELTRA,S.DUFOUR, REMARK 1 AUTH 2 I.DE MENDEZ,P.MANCEAU,A.TERTRE,F.MOREAU,D.COMPERE, REMARK 1 AUTH 3 A.C.DUBLANCHET,M.O'GARA REMARK 1 TITL CRYSTAL STRUCTURES OF NOVEL NON-PEPTIDIC, NON-ZINC CHELATING REMARK 1 TITL 2 INHIBITORS BOUND TO MMP-12 REMARK 1 REF J.MOL.BIOL. V. 341 1063 2004 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 15289103 REMARK 1 DOI 10.1016/J.JMB.2004.06.039 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 20425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1400 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 : 2564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 361 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.290 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 3DNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20603 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6000 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 FOR SHELL : NULL 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 1I76 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROPLETS WERE MADE BY MIXING REMARK 280 1.5-3.0ML OF PROTEIN/INHIBITOR SOLUTION WITH 5ML OF PEG SOLUTION REMARK 280 (10% PEG6000, 0.2M MES-NAOH, 0.02% NAN3, PH6.0). DROPLETS WERE REMARK 280 CONCENTRATED AGAINST A RESERVOIR BUFFER CONTAINING 1.0-2.0M REMARK 280 SODIUM PHOSPHATE, 0.02% NAN3, PH6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.69200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 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 N THR B 82 O GLY B 204 2.18 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 PRO A 83 172.91 -52.68 REMARK 500 ARG A 145 -129.77 40.79 REMARK 500 HIS A 147 35.40 -142.95 REMARK 500 ASN A 157 -164.13 63.78 REMARK 500 ALA A 161 171.86 178.37 REMARK 500 THR A 185 -169.43 -119.61 REMARK 500 PRO B 83 154.52 -44.86 REMARK 500 ARG B 145 -127.93 37.91 REMARK 500 ASN B 157 -156.80 62.00 REMARK 500 ALA B 161 179.90 179.10 REMARK 500 THR B 185 -168.61 -123.56 REMARK 500 ALA B 220 97.87 -165.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 1086 REMARK 615 HOH A 1142 REMARK 615 HOH B 1086 REMARK 615 HOH B 1130 REMARK 615 HOH B 1131 REMARK 615 HOH B 1152 REMARK 615 HOH B 1160 REMARK 615 HOH B 1166 REMARK 615 HOH B 1171 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 996 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 137 O REMARK 620 2 GLY A 169 O 167.9 REMARK 620 3 GLY A 171 O 92.7 94.8 REMARK 620 4 ASP A 173 OD1 89.2 100.5 88.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 147 NE2 REMARK 620 2 ASP A 149 OD2 111.6 REMARK 620 3 HIS A 162 NE2 111.9 112.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 997 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 154 OD1 REMARK 620 2 GLY A 155 O 83.3 REMARK 620 3 ASN A 157 O 84.4 82.3 REMARK 620 4 ILE A 159 O 94.6 176.3 94.5 REMARK 620 5 ASP A 177 OD2 97.1 86.2 168.2 97.0 REMARK 620 6 GLU A 180 OE2 154.6 106.4 74.0 74.3 106.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 197 NE2 REMARK 620 2 HIS A 201 NE2 108.6 REMARK 620 3 HIS A 207 NE2 110.4 103.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 996 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 137 O REMARK 620 2 GLY B 169 O 165.7 REMARK 620 3 GLY B 171 O 96.5 92.6 REMARK 620 4 ASP B 173 OD1 89.5 101.5 90.1 REMARK 620 5 HOH B1051 O 86.6 82.3 168.0 101.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 998 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 147 NE2 REMARK 620 2 ASP B 149 OD2 107.0 REMARK 620 3 HIS B 162 NE2 111.5 119.6 REMARK 620 4 HOH B1086 O 64.3 171.1 65.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 997 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 154 OD1 REMARK 620 2 GLY B 155 O 95.9 REMARK 620 3 ASN B 157 O 90.8 90.6 REMARK 620 4 ILE B 159 O 89.1 174.4 86.8 REMARK 620 5 ASP B 177 OD2 90.4 85.0 175.5 97.6 REMARK 620 6 GLU B 180 OE2 155.8 101.2 72.2 73.3 107.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 197 NE2 REMARK 620 2 HIS B 201 NE2 110.2 REMARK 620 3 HIS B 207 NE2 103.4 99.8 REMARK 620 4 HOH B1000 O 111.4 110.6 120.6 REMARK 620 N 1 2 3 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 996 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 997 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 996 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 997 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AXA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AXA B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XUC RELATED DB: PDB REMARK 900 CRYSTAL COMPLEXES OF MMP-13 WITH NON-ZINC CHELATING INHIBITORS REMARK 900 RELATED ID: 1XUD RELATED DB: PDB REMARK 900 RELATED ID: 1XUR RELATED DB: PDB REMARK 900 RELATED ID: 2OW9 RELATED DB: PDB REMARK 900 CRYSTAL COMPLEXES OF MMP-13 WITH NON-ZINC CHELATING INHIBITORS REMARK 900 RELATED ID: 2OZR RELATED DB: PDB REMARK 900 RELATED ID: 1UTT RELATED DB: PDB REMARK 900 CRYSTAL COMPLEXES OF MMP-12 WITH NON-ZINC CHELATING INHIBITORS REMARK 900 RELATED ID: 1UTZ RELATED DB: PDB DBREF 3DNG A 80 242 UNP P22894 MMP8_HUMAN 100 262 DBREF 3DNG B 80 242 UNP P22894 MMP8_HUMAN 100 262 SEQRES 1 A 163 MET LEU THR PRO GLY ASN PRO LYS TRP GLU ARG THR ASN SEQRES 2 A 163 LEU THR TYR ARG ILE ARG ASN TYR THR PRO GLN LEU SER SEQRES 3 A 163 GLU ALA GLU VAL GLU ARG ALA ILE LYS ASP ALA PHE GLU SEQRES 4 A 163 LEU TRP SER VAL ALA SER PRO LEU ILE PHE THR ARG ILE SEQRES 5 A 163 SER GLN GLY GLU ALA ASP ILE ASN ILE ALA PHE TYR GLN SEQRES 6 A 163 ARG ASP HIS GLY ASP ASN SER PRO PHE ASP GLY PRO ASN SEQRES 7 A 163 GLY ILE LEU ALA HIS ALA PHE GLN PRO GLY GLN GLY ILE SEQRES 8 A 163 GLY GLY ASP ALA HIS PHE ASP ALA GLU GLU THR TRP THR SEQRES 9 A 163 ASN THR SER ALA ASN TYR ASN LEU PHE LEU VAL ALA ALA SEQRES 10 A 163 HIS GLU PHE GLY HIS SER LEU GLY LEU ALA HIS SER SER SEQRES 11 A 163 ASP PRO GLY ALA LEU MET TYR PRO ASN TYR ALA PHE ARG SEQRES 12 A 163 GLU THR SER ASN TYR SER LEU PRO GLN ASP ASP ILE ASP SEQRES 13 A 163 GLY ILE GLN ALA ILE TYR GLY SEQRES 1 B 163 MET LEU THR PRO GLY ASN PRO LYS TRP GLU ARG THR ASN SEQRES 2 B 163 LEU THR TYR ARG ILE ARG ASN TYR THR PRO GLN LEU SER SEQRES 3 B 163 GLU ALA GLU VAL GLU ARG ALA ILE LYS ASP ALA PHE GLU SEQRES 4 B 163 LEU TRP SER VAL ALA SER PRO LEU ILE PHE THR ARG ILE SEQRES 5 B 163 SER GLN GLY GLU ALA ASP ILE ASN ILE ALA PHE TYR GLN SEQRES 6 B 163 ARG ASP HIS GLY ASP ASN SER PRO PHE ASP GLY PRO ASN SEQRES 7 B 163 GLY ILE LEU ALA HIS ALA PHE GLN PRO GLY GLN GLY ILE SEQRES 8 B 163 GLY GLY ASP ALA HIS PHE ASP ALA GLU GLU THR TRP THR SEQRES 9 B 163 ASN THR SER ALA ASN TYR ASN LEU PHE LEU VAL ALA ALA SEQRES 10 B 163 HIS GLU PHE GLY HIS SER LEU GLY LEU ALA HIS SER SER SEQRES 11 B 163 ASP PRO GLY ALA LEU MET TYR PRO ASN TYR ALA PHE ARG SEQRES 12 B 163 GLU THR SER ASN TYR SER LEU PRO GLN ASP ASP ILE ASP SEQRES 13 B 163 GLY ILE GLN ALA ILE TYR GLY HET CA A 996 1 HET CA A 997 1 HET ZN A 998 1 HET ZN A 999 1 HET AXA A 1 33 HET CA B 996 1 HET CA B 997 1 HET ZN B 998 1 HET ZN B 999 1 HET AXA B 2 33 HETNAM CA CALCIUM ION HETNAM ZN ZINC ION HETNAM AXA (5S)-5-(2-AMINO-2-OXOETHYL)-4-OXO-N-[(3-OXO-3,4- HETNAM 2 AXA DIHYDRO-2H-1,4-BENZOXAZIN-6-YL)METHYL]-3,4,5,6,7,8- HETNAM 3 AXA HEXAHYDRO[1]BENZOTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE FORMUL 3 CA 4(CA 2+) FORMUL 5 ZN 4(ZN 2+) FORMUL 7 AXA 2(C22 H21 N5 O5 S) FORMUL 13 HOH *361(H2 O) HELIX 1 1 SER A 105 VAL A 122 1 18 HELIX 2 2 ASN A 190 GLY A 204 1 15 HELIX 3 3 PRO A 230 GLY A 242 1 13 HELIX 4 4 SER B 105 VAL B 122 1 18 HELIX 5 5 ASN B 190 LEU B 203 1 14 HELIX 6 6 PRO B 230 GLY B 242 1 13 SHEET 1 A 5 ILE A 127 ARG A 130 0 SHEET 2 A 5 ASN A 92 ILE A 97 1 N LEU A 93 O THR A 129 SHEET 3 A 5 ILE A 138 TYR A 143 1 O ILE A 140 N ARG A 96 SHEET 4 A 5 ALA A 174 ASP A 177 1 O ALA A 174 N ASN A 139 SHEET 5 A 5 ALA A 161 ALA A 163 -1 N HIS A 162 O HIS A 175 SHEET 1 B 5 ILE B 127 ARG B 130 0 SHEET 2 B 5 ASN B 92 ILE B 97 1 N LEU B 93 O THR B 129 SHEET 3 B 5 ILE B 138 TYR B 143 1 O ILE B 140 N ARG B 96 SHEET 4 B 5 ALA B 174 ASP B 177 1 O ALA B 174 N ASN B 139 SHEET 5 B 5 ALA B 161 ALA B 163 -1 N HIS B 162 O HIS B 175 LINK O ASP A 137 CA CA A 996 1555 1555 2.55 LINK NE2 HIS A 147 ZN ZN A 998 1555 1555 2.13 LINK OD2 ASP A 149 ZN ZN A 998 1555 1555 2.04 LINK OD1 ASP A 154 CA CA A 997 1555 1555 2.55 LINK O GLY A 155 CA CA A 997 1555 1555 2.44 LINK O ASN A 157 CA CA A 997 1555 1555 2.45 LINK O ILE A 159 CA CA A 997 1555 1555 2.40 LINK NE2 HIS A 162 ZN ZN A 998 1555 1555 2.17 LINK O GLY A 169 CA CA A 996 1555 1555 2.55 LINK O GLY A 171 CA CA A 996 1555 1555 2.56 LINK OD1 ASP A 173 CA CA A 996 1555 1555 2.60 LINK OD2 ASP A 177 CA CA A 997 1555 1555 2.61 LINK OE2 GLU A 180 CA CA A 997 1555 1555 2.79 LINK NE2 HIS A 197 ZN ZN A 999 1555 1555 2.28 LINK NE2 HIS A 201 ZN ZN A 999 1555 1555 2.23 LINK NE2 HIS A 207 ZN ZN A 999 1555 1555 2.17 LINK O ASP B 137 CA CA B 996 1555 1555 2.50 LINK NE2 HIS B 147 ZN ZN B 998 1555 1555 2.12 LINK OD2 ASP B 149 ZN ZN B 998 1555 1555 2.09 LINK OD1 ASP B 154 CA CA B 997 1555 1555 2.58 LINK O GLY B 155 CA CA B 997 1555 1555 2.46 LINK O ASN B 157 CA CA B 997 1555 1555 2.49 LINK O ILE B 159 CA CA B 997 1555 1555 2.43 LINK NE2 HIS B 162 ZN ZN B 998 1555 1555 2.15 LINK O GLY B 169 CA CA B 996 1555 1555 2.54 LINK O GLY B 171 CA CA B 996 1555 1555 2.56 LINK OD1 ASP B 173 CA CA B 996 1555 1555 2.61 LINK OD2 ASP B 177 CA CA B 997 1555 1555 2.56 LINK OE2 GLU B 180 CA CA B 997 1555 1555 2.65 LINK NE2 HIS B 197 ZN ZN B 999 1555 1555 2.27 LINK NE2 HIS B 201 ZN ZN B 999 1555 1555 2.28 LINK NE2 HIS B 207 ZN ZN B 999 1555 1555 2.13 LINK CA CA B 996 O HOH B1051 1555 1555 2.82 LINK ZN ZN B 998 O HOH B1086 1555 1555 2.22 LINK ZN ZN B 999 O HOH B1000 1555 1555 2.30 CISPEP 1 ASN A 188 TYR A 189 0 -0.22 CISPEP 2 ASN B 188 TYR B 189 0 -0.05 SITE 1 AC1 4 ASP A 137 GLY A 169 GLY A 171 ASP A 173 SITE 1 AC2 6 ASP A 154 GLY A 155 ASN A 157 ILE A 159 SITE 2 AC2 6 ASP A 177 GLU A 180 SITE 1 AC3 4 HIS A 147 ASP A 149 HIS A 162 HIS A 175 SITE 1 AC4 3 HIS A 197 HIS A 201 HIS A 207 SITE 1 AC5 4 ASP B 137 GLY B 169 GLY B 171 ASP B 173 SITE 1 AC6 6 ASP B 154 GLY B 155 ASN B 157 ILE B 159 SITE 2 AC6 6 ASP B 177 GLU B 180 SITE 1 AC7 4 HIS B 147 ASP B 149 HIS B 162 HIS B 175 SITE 1 AC8 3 HIS B 197 HIS B 201 HIS B 207 SITE 1 AC9 15 PHE A 192 LEU A 193 HIS A 197 ALA A 213 SITE 2 AC9 15 LEU A 214 TYR A 216 PRO A 217 ASN A 218 SITE 3 AC9 15 TYR A 219 ALA A 220 PHE A 221 ARG A 222 SITE 4 AC9 15 THR A 224 TYR A 227 SER A 228 SITE 1 BC1 14 LEU B 193 HIS B 197 ALA B 213 LEU B 214 SITE 2 BC1 14 TYR B 216 PRO B 217 ASN B 218 TYR B 219 SITE 3 BC1 14 ALA B 220 PHE B 221 ARG B 222 THR B 224 SITE 4 BC1 14 TYR B 227 SER B 228 CRYST1 42.344 69.384 52.707 90.00 92.35 90.00 P 1 21 1 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 0.023616 0.000000 0.000969 0.00000 SCALE2 0.000000 0.014413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018989 0.00000