PDB Short entry for 3I7G HEADER HYDROLASE 08-JUL-09 3I7G TITLE MMP-13 IN COMPLEX WITH A NON ZINC-CHELATING INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 104-274; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-13, MMP-13; COMPND 6 EC: 3.4.24.-; COMPND 7 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: MMP13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEASE, CALCIUM, COLLAGEN DEGRADATION, DISEASE MUTATION, DISULFIDE KEYWDS 2 BOND, EXTRACELLULAR MATRIX, GLYCOPROTEIN, HYDROLASE, METAL-BINDING, KEYWDS 3 METALLOPROTEASE, POLYMORPHISM, SECRETED, ZINC, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR N.A.FARROW REVDAT 3 21-FEB-24 3I7G 1 REMARK LINK REVDAT 2 08-SEP-09 3I7G 1 JRNL REVDAT 1 01-SEP-09 3I7G 0 JRNL AUTH A.HEIM-RIETHER,S.J.TAYLOR,S.LIANG,D.A.GAO,Z.XIONG, JRNL AUTH 2 E.MICHAEL AUGUST,B.K.COLLINS,B.T.FARMER,K.HAVERTY, JRNL AUTH 3 M.HILL-DRZEWI,H.D.JUNKER,S.MARIANA MARGARIT,N.MOSS, JRNL AUTH 4 T.NEUMANN,J.R.PROUDFOOT,L.S.KEENAN,R.SEKUL,Q.ZHANG,J.LI, JRNL AUTH 5 N.A.FARROW JRNL TITL IMPROVING POTENCY AND SELECTIVITY OF A NEW CLASS OF JRNL TITL 2 NON-ZN-CHELATING MMP-13 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 19 5321 2009 JRNL REFN ISSN 0960-894X JRNL PMID 19692239 JRNL DOI 10.1016/J.BMCL.2009.07.151 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.4_6 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 24413 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 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 : 1171 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.3790 - 3.8980 0.99 3113 167 0.1670 0.1980 REMARK 3 2 3.8980 - 3.0950 1.00 3069 151 0.1600 0.2150 REMARK 3 3 3.0950 - 2.7040 1.00 3060 140 0.1910 0.2600 REMARK 3 4 2.7040 - 2.4570 1.00 3023 141 0.1730 0.2520 REMARK 3 5 2.4570 - 2.2810 1.00 3025 164 0.1600 0.2170 REMARK 3 6 2.2810 - 2.1460 0.99 3004 131 0.1620 0.2300 REMARK 3 7 2.1460 - 2.0390 0.97 2897 156 0.1740 0.2370 REMARK 3 8 2.0390 - 1.9500 0.68 2051 121 0.1820 0.2790 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 59.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.850 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.96100 REMARK 3 B22 (A**2) : 0.89000 REMARK 3 B33 (A**2) : -3.85100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.06200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2743 REMARK 3 ANGLE : 1.237 3725 REMARK 3 CHIRALITY : 0.082 373 REMARK 3 PLANARITY : 0.007 485 REMARK 3 DIHEDRAL : 18.530 947 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3I7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054059. 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 : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24419 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.650 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 45.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.88500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.88500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.05000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -301.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 9.26050 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 144.39843 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 GLY A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 HIS A 251 REMARK 465 PRO A 273 REMARK 465 ASN A 274 REMARK 465 THR B 247 REMARK 465 GLY B 248 REMARK 465 LYS B 249 REMARK 465 ASP B 270 REMARK 465 GLU B 271 REMARK 465 ASP B 272 REMARK 465 PRO B 273 REMARK 465 ASN B 274 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 O HOH B 313 O HOH B 313 2657 1.65 REMARK 500 O HOH A 332 O HOH A 332 2657 1.92 REMARK 500 O HOH A 323 O HOH B 49 2657 2.02 REMARK 500 O HOH B 298 O HOH B 313 2657 2.19 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 LYS A 170 -128.89 45.66 REMARK 500 SER A 182 179.91 77.45 REMARK 500 ASN A 194 -115.05 54.60 REMARK 500 SER A 210 -156.82 -131.32 REMARK 500 THR B 110 84.26 -61.95 REMARK 500 LYS B 170 -134.44 46.84 REMARK 500 TYR B 176 74.00 -112.80 REMARK 500 SER B 182 -174.89 71.78 REMARK 500 ASN B 194 -123.69 62.87 REMARK 500 SER B 210 -138.80 -119.99 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 A1261 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 FMT A 2 O1 REMARK 620 2 FMT A 2 O2 55.3 REMARK 620 3 HIS A 222 NE2 95.2 124.1 REMARK 620 4 HIS A 226 NE2 94.8 125.4 100.5 REMARK 620 5 HIS A 232 NE2 140.7 86.8 117.0 100.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1263 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 203 O 160.4 REMARK 620 3 ASP A 203 OD2 104.4 68.1 REMARK 620 4 GLU A 205 O 75.4 89.6 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1265 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 158.4 REMARK 620 3 GLY A 196 O 83.0 93.1 REMARK 620 4 ASP A 198 OD1 90.0 111.5 94.7 REMARK 620 5 HOH A 277 O 97.4 80.4 163.4 101.9 REMARK 620 6 HOH A 319 O 89.4 69.5 69.1 163.7 94.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1262 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 111.7 REMARK 620 3 HIS A 187 NE2 110.6 117.4 REMARK 620 4 HIS A 200 ND1 107.5 95.8 112.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1264 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 84.7 REMARK 620 3 SER A 182 O 84.1 82.9 REMARK 620 4 LEU A 184 O 88.1 170.4 90.0 REMARK 620 5 ASP A 202 OD2 96.0 96.9 179.8 90.2 REMARK 620 6 GLU A 205 OE2 160.1 89.8 76.2 94.9 103.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2261 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 FMT B 3 O1 REMARK 620 2 HIS B 222 NE2 136.3 REMARK 620 3 HIS B 226 NE2 106.4 103.3 REMARK 620 4 HIS B 232 NE2 91.5 112.3 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2263 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 128 OD2 REMARK 620 2 ASP B 203 O 153.5 REMARK 620 3 ASP B 203 OD2 111.2 67.5 REMARK 620 4 GLU B 205 O 73.5 80.5 98.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2265 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 169.3 REMARK 620 3 GLY B 196 O 91.3 93.9 REMARK 620 4 ASP B 198 OD1 88.2 100.7 94.7 REMARK 620 5 HOH B 292 O 84.5 87.6 76.3 168.3 REMARK 620 6 HOH B 311 O 92.0 80.8 166.0 99.0 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2262 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 115.4 REMARK 620 3 HIS B 187 NE2 111.8 114.3 REMARK 620 4 HIS B 200 ND1 108.6 90.5 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2264 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 82.2 REMARK 620 3 SER B 182 O 85.5 89.1 REMARK 620 4 LEU B 184 O 94.2 175.7 88.4 REMARK 620 5 ASP B 202 OD2 93.5 87.0 176.1 95.5 REMARK 620 6 GLU B 205 OE1 169.4 94.0 84.5 89.2 96.2 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 1261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 732 A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2262 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2263 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2264 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2265 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I7I RELATED DB: PDB REMARK 900 MMP-13 IN COMPLEX WITH A NON ZINC-CHELATING INHIBITOR, 517 DBREF 3I7G A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 3I7G B 104 274 UNP P45452 MMP13_HUMAN 104 274 SEQRES 1 A 171 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 171 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 171 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 171 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 171 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 171 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 171 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 171 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 171 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 171 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 171 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 171 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 171 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU ASP SEQRES 14 A 171 PRO ASN SEQRES 1 B 171 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 B 171 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 B 171 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 B 171 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 B 171 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 B 171 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 171 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 B 171 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 B 171 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 B 171 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 B 171 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 B 171 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 B 171 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU ASP SEQRES 14 B 171 PRO ASN HET ZN A1261 1 HET ZN A1262 1 HET CA A1263 1 HET CA A1264 1 HET CA A1265 1 HET FMT A 2 3 HET 732 A 999 26 HET ZN B2261 1 HET ZN B2262 1 HET CA B2263 1 HET CA B2264 1 HET CA B2265 1 HET FMT B 3 3 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM FMT FORMIC ACID HETNAM 732 5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2- HETNAM 2 732 (METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 FMT 2(C H2 O2) FORMUL 9 732 C20 H23 CL N2 O3 FORMUL 16 HOH *346(H2 O) HELIX 1 1 THR A 130 ASP A 147 1 18 HELIX 2 2 LEU A 216 GLY A 229 1 14 HELIX 3 3 PRO A 255 GLY A 267 1 13 HELIX 4 4 THR B 130 ASP B 147 1 18 HELIX 5 5 LEU B 216 LEU B 228 1 13 HELIX 6 6 PRO B 255 GLY B 267 1 13 SHEET 1 A 5 ASN A 152 LEU A 156 0 SHEET 2 A 5 ASN A 117 ILE A 122 1 N TYR A 120 O LEU A 156 SHEET 3 A 5 ILE A 163 GLY A 168 1 O ILE A 165 N ARG A 121 SHEET 4 A 5 ALA A 199 ASP A 202 1 O PHE A 201 N SER A 166 SHEET 5 A 5 ALA A 186 ALA A 188 -1 N HIS A 187 O HIS A 200 SHEET 1 B 2 TRP A 207 THR A 208 0 SHEET 2 B 2 TYR A 214 ASN A 215 1 O TYR A 214 N THR A 208 SHEET 1 C 2 LEU A 230 ASP A 231 0 SHEET 2 C 2 ASN B 105 VAL B 106 -1 O ASN B 105 N ASP A 231 SHEET 1 D 5 ASN B 152 ARG B 155 0 SHEET 2 D 5 ASN B 117 ILE B 122 1 N LEU B 118 O ASN B 152 SHEET 3 D 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121 SHEET 4 D 5 ALA B 199 ASP B 202 1 O PHE B 201 N SER B 166 SHEET 5 D 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200 SHEET 1 E 2 TRP B 207 THR B 208 0 SHEET 2 E 2 TYR B 214 ASN B 215 1 O TYR B 214 N THR B 208 LINK O1 FMT A 2 ZN ZN A1261 1555 1555 2.26 LINK O2 FMT A 2 ZN ZN A1261 1555 1555 2.34 LINK OD2 ASP A 128 CA CA A1263 1555 1555 2.67 LINK O ASP A 162 CA CA A1265 1555 1555 2.58 LINK NE2 HIS A 172 ZN ZN A1262 1555 1555 2.05 LINK OD2 ASP A 174 ZN ZN A1262 1555 1555 2.01 LINK OD1 ASP A 179 CA CA A1264 1555 1555 2.50 LINK O GLY A 180 CA CA A1264 1555 1555 2.32 LINK O SER A 182 CA CA A1264 1555 1555 2.45 LINK O LEU A 184 CA CA A1264 1555 1555 2.38 LINK NE2 HIS A 187 ZN ZN A1262 1555 1555 2.05 LINK O ASN A 194 CA CA A1265 1555 1555 2.55 LINK O GLY A 196 CA CA A1265 1555 1555 2.52 LINK OD1 ASP A 198 CA CA A1265 1555 1555 2.55 LINK ND1 HIS A 200 ZN ZN A1262 1555 1555 1.98 LINK OD2 ASP A 202 CA CA A1264 1555 1555 2.34 LINK O ASP A 203 CA CA A1263 1555 1555 2.88 LINK OD2 ASP A 203 CA CA A1263 1555 1555 2.89 LINK O GLU A 205 CA CA A1263 1555 1555 2.65 LINK OE2 GLU A 205 CA CA A1264 1555 1555 2.42 LINK NE2 HIS A 222 ZN ZN A1261 1555 1555 2.08 LINK NE2 HIS A 226 ZN ZN A1261 1555 1555 2.05 LINK NE2 HIS A 232 ZN ZN A1261 1555 1555 2.12 LINK O HOH A 277 CA CA A1265 1555 1555 2.52 LINK O HOH A 319 CA CA A1265 1555 1555 2.79 LINK O1 FMT B 3 ZN ZN B2261 1555 1555 2.35 LINK OD2 ASP B 128 CA CA B2263 1555 1555 2.68 LINK O ASP B 162 CA CA B2265 1555 1555 2.41 LINK NE2 HIS B 172 ZN ZN B2262 1555 1555 2.02 LINK OD2 ASP B 174 ZN ZN B2262 1555 1555 1.99 LINK OD1 ASP B 179 CA CA B2264 1555 1555 2.45 LINK O GLY B 180 CA CA B2264 1555 1555 2.37 LINK O SER B 182 CA CA B2264 1555 1555 2.47 LINK O LEU B 184 CA CA B2264 1555 1555 2.31 LINK NE2 HIS B 187 ZN ZN B2262 1555 1555 2.09 LINK O ASN B 194 CA CA B2265 1555 1555 2.51 LINK O GLY B 196 CA CA B2265 1555 1555 2.32 LINK OD1 ASP B 198 CA CA B2265 1555 1555 2.49 LINK ND1 HIS B 200 ZN ZN B2262 1555 1555 2.17 LINK OD2 ASP B 202 CA CA B2264 1555 1555 2.35 LINK O ASP B 203 CA CA B2263 1555 1555 2.96 LINK OD2 ASP B 203 CA CA B2263 1555 1555 2.93 LINK O GLU B 205 CA CA B2263 1555 1555 2.92 LINK OE1 GLU B 205 CA CA B2264 1555 1555 2.25 LINK NE2 HIS B 222 ZN ZN B2261 1555 1555 2.10 LINK NE2 HIS B 226 ZN ZN B2261 1555 1555 2.05 LINK NE2 HIS B 232 ZN ZN B2261 1555 1555 2.16 LINK O HOH B 292 CA CA B2265 1555 1555 2.65 LINK O HOH B 311 CA CA B2265 1555 1555 2.51 SITE 1 AC1 4 FMT A 2 HIS A 222 HIS A 226 HIS A 232 SITE 1 AC2 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC3 4 THR A 126 ASP A 128 ASP A 203 GLU A 205 SITE 1 AC4 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC4 6 ASP A 202 GLU A 205 SITE 1 AC5 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC5 6 HOH A 277 HOH A 319 SITE 1 AC6 7 ALA A 186 HIS A 222 GLU A 223 HIS A 226 SITE 2 AC6 7 HIS A 232 732 A 999 ZN A1261 SITE 1 AC7 13 FMT A 2 LEU A 156 GLY A 183 LEU A 185 SITE 2 AC7 13 ALA A 186 TYR A 214 HIS A 222 GLU A 223 SITE 3 AC7 13 LEU A 239 PHE A 241 ILE A 243 TYR A 244 SITE 4 AC7 13 HOH A 527 SITE 1 AC8 4 FMT B 3 HIS B 222 HIS B 226 HIS B 232 SITE 1 AC9 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 BC1 5 HOH A 308 THR B 126 ASP B 128 ASP B 203 SITE 2 BC1 5 GLU B 205 SITE 1 BC2 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 BC2 6 ASP B 202 GLU B 205 SITE 1 BC3 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 BC3 6 HOH B 292 HOH B 311 SITE 1 BC4 6 ALA B 186 HIS B 222 GLU B 223 HIS B 226 SITE 2 BC4 6 HIS B 232 ZN B2261 CRYST1 133.770 36.100 95.333 90.00 130.77 90.00 C 1 2 1 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 0.007476 0.000000 0.006446 0.00000 SCALE2 0.000000 0.027701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013851 0.00000