HEADER HYDROLASE 22-SEP-08 3ELM TITLE CRYSTAL STRUCTURE OF MMP-13 COMPLEXED WITH INHIBITOR 24F COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 104 TO 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3B KEYWDS METALLO-ENZYME, MMP-13, CARBOXYLATE INHIBITOR, CALCIUM, COLLAGEN KEYWDS 2 DEGRADATION, DISEASE MUTATION, EXTRACELLULAR MATRIX, GLYCOPROTEIN, KEYWDS 3 HYDROLASE, METAL-BINDING, METALLOPROTEASE, POLYMORPHISM, PROTEASE, KEYWDS 4 SECRETED, ZINC, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR R.KULATHILA,L.MONOVICH,J.KOEHN REVDAT 3 21-FEB-24 3ELM 1 REMARK LINK REVDAT 2 25-OCT-17 3ELM 1 REMARK REVDAT 1 21-JUL-09 3ELM 0 JRNL AUTH L.G.MONOVICH,R.A.TOMMASI,R.A.FUJIMOTO,V.BLANCUZZI,K.CLARK, JRNL AUTH 2 W.D.CORNELL,R.DOTI,J.DOUGHTY,J.FANG,D.FARLEY,J.FITT,V.GANU, JRNL AUTH 3 R.GOLDBERG,R.GOLDSTEIN,S.LAVOIE,R.KULATHILA,W.MACCHIA, JRNL AUTH 4 D.T.PARKER,R.MELTON,E.O'BYRNE,G.PASTOR,T.PELLAS,E.QUADROS, JRNL AUTH 5 N.REEL,D.M.ROLAND,Y.SAKANE,H.SINGH,J.SKILES,J.SOMERS, JRNL AUTH 6 K.TOSCANO,A.WIGG,S.ZHOU,L.ZHU,W.C.SHIEH,S.XUE,L.W.MCQUIRE JRNL TITL DISCOVERY OF POTENT, SELECTIVE, AND ORALLY ACTIVE CARBOXYLIC JRNL TITL 2 ACID BASED INHIBITORS OF MATRIX METALLOPROTEINASE-13 JRNL REF J.MED.CHEM. V. 52 3523 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19422229 JRNL DOI 10.1021/JM801394M REMARK 2 REMARK 2 RESOLUTION. 1.90 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 725073.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 25975 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 + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2588 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3066 REMARK 3 BIN R VALUE (WORKING SET) : 0.1630 REMARK 3 BIN FREE R VALUE : 0.2130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 355 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2631 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.71000 REMARK 3 B22 (A**2) : -0.47000 REMARK 3 B33 (A**2) : -1.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.02 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.840 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 41.97 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : 24F.PARAMETER REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : 24F.TOPOLOGY REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3ELM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MULTI-LAYER MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26969 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2460 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.11900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 46.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 6K, 0.1M TRIS, 1.2M NAACETATE, REMARK 280 2% GLYCEROL, 15 MM CACL2, 10 UM ZN(AC)2, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K 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 67.25000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.03500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.25000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.03500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -157.0 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 10.79530 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 144.68613 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 2890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 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 THR A 247 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 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 A 1067 O HOH B 1143 2657 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 LYS A 170 -126.73 41.94 REMARK 500 SER A 182 -172.26 63.13 REMARK 500 ASN A 194 -116.45 52.26 REMARK 500 LYS B 170 -132.87 45.11 REMARK 500 SER B 182 -168.62 65.04 REMARK 500 ASN B 194 -119.62 58.95 REMARK 500 SER B 210 -150.90 -136.19 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 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 203 O 173.3 REMARK 620 3 ASP A 203 OD2 97.3 80.2 REMARK 620 4 GLU A 205 O 85.5 90.4 121.3 REMARK 620 5 HOH A1184 O 99.5 87.2 106.3 131.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 146 O REMARK 620 2 THR A 149 O 83.0 REMARK 620 3 HOH A1003 O 173.3 97.5 REMARK 620 4 HOH A1007 O 104.4 84.4 82.3 REMARK 620 5 HOH A1020 O 87.4 85.7 85.9 163.5 REMARK 620 6 HOH A1187 O 86.6 169.5 93.1 96.8 95.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 164.0 REMARK 620 3 GLY A 196 O 93.5 98.0 REMARK 620 4 ASP A 198 OD1 88.8 101.3 94.6 REMARK 620 5 HOH A1132 O 87.4 83.0 82.6 175.2 REMARK 620 6 HOH A1183 O 88.9 78.0 170.4 94.7 88.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 113.4 REMARK 620 3 HIS A 187 NE2 113.6 116.2 REMARK 620 4 HIS A 200 ND1 108.0 94.1 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 85.8 REMARK 620 3 SER A 182 O 82.6 83.2 REMARK 620 4 LEU A 184 O 93.4 177.8 94.6 REMARK 620 5 ASP A 202 OD2 92.9 89.7 171.8 92.4 REMARK 620 6 GLU A 205 OE2 171.6 90.3 89.5 90.2 94.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 103.2 REMARK 620 3 HIS A 232 NE2 110.8 98.5 REMARK 620 4 24F A 400 O21 113.1 136.1 91.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 128 OD2 REMARK 620 2 ASP B 203 O 169.9 REMARK 620 3 ASP B 203 OD2 97.7 79.0 REMARK 620 4 GLU B 205 O 85.8 87.4 118.6 REMARK 620 5 HOH B1143 O 102.0 88.1 106.8 132.5 REMARK 620 6 HOH B1201 O 90.7 94.9 163.7 75.8 57.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 167.4 REMARK 620 3 GLY B 196 O 90.5 100.0 REMARK 620 4 ASP B 198 OD1 91.4 94.6 94.0 REMARK 620 5 HOH B1185 O 88.5 86.9 78.7 172.7 REMARK 620 6 HOH B1186 O 93.0 75.3 166.9 98.6 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 112.6 REMARK 620 3 HIS B 187 NE2 112.1 114.1 REMARK 620 4 HIS B 200 ND1 110.9 93.8 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 87.3 REMARK 620 3 SER B 182 O 81.3 89.1 REMARK 620 4 LEU B 184 O 96.0 176.7 91.2 REMARK 620 5 ASP B 202 OD2 94.6 85.8 173.6 94.1 REMARK 620 6 GLU B 205 OE2 166.7 86.1 87.1 90.7 96.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 110.5 REMARK 620 3 HIS B 232 NE2 111.8 101.7 REMARK 620 4 24F B 400 O21 112.9 127.0 89.2 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 ZN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 24F A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 24F B 400 DBREF 3ELM A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 3ELM 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 A 300 1 HET ZN A 301 1 HET CA A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HET 24F A 400 34 HET ZN B 300 1 HET ZN B 301 1 HET CA B 302 1 HET CA B 303 1 HET CA B 304 1 HET 24F B 400 34 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM 24F (2R)-({[5-(4-ETHOXYPHENYL)THIOPHEN-2- HETNAM 2 24F YL]SULFONYL}AMINO){1-[(1-METHYLETHOXY) HETNAM 3 24F CARBONYL]PIPERIDIN-4-YL}ETHANOIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 7(CA 2+) FORMUL 9 24F 2(C23 H30 N2 O7 S2) FORMUL 16 HOH *239(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 5 ASN B 152 ARG B 155 0 SHEET 2 C 5 ASN B 117 ILE B 122 1 N LEU B 118 O ASN B 152 SHEET 3 C 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121 SHEET 4 C 5 ALA B 199 ASP B 202 1 O PHE B 201 N GLY B 168 SHEET 5 C 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200 SHEET 1 D 2 TRP B 207 THR B 208 0 SHEET 2 D 2 TYR B 214 ASN B 215 1 O TYR B 214 N THR B 208 LINK OD2 ASP A 128 CA CA A 303 1555 1555 2.35 LINK O SER A 146 CA CA A 305 1555 1555 2.43 LINK O THR A 149 CA CA A 305 1555 1555 2.26 LINK O ASP A 162 CA CA A 304 1555 1555 2.42 LINK NE2 HIS A 172 ZN ZN A 301 1555 1555 1.92 LINK OD2 ASP A 174 ZN ZN A 301 1555 1555 1.98 LINK OD1 ASP A 179 CA CA A 302 1555 1555 2.37 LINK O GLY A 180 CA CA A 302 1555 1555 2.27 LINK O SER A 182 CA CA A 302 1555 1555 2.33 LINK O LEU A 184 CA CA A 302 1555 1555 2.33 LINK NE2 HIS A 187 ZN ZN A 301 1555 1555 2.04 LINK O ASN A 194 CA CA A 304 1555 1555 2.36 LINK O GLY A 196 CA CA A 304 1555 1555 2.23 LINK OD1 ASP A 198 CA CA A 304 1555 1555 2.44 LINK ND1 HIS A 200 ZN ZN A 301 1555 1555 1.99 LINK OD2 ASP A 202 CA CA A 302 1555 1555 2.30 LINK O ASP A 203 CA CA A 303 1555 1555 2.46 LINK OD2 ASP A 203 CA CA A 303 1555 1555 2.43 LINK OE2 GLU A 205 CA CA A 302 1555 1555 2.16 LINK O GLU A 205 CA CA A 303 1555 1555 2.34 LINK NE2 HIS A 222 ZN ZN A 300 1555 1555 2.09 LINK NE2 HIS A 226 ZN ZN A 300 1555 1555 2.06 LINK NE2 HIS A 232 ZN ZN A 300 1555 1555 1.98 LINK ZN ZN A 300 O21 24F A 400 1555 1555 2.12 LINK CA CA A 303 O HOH A1184 1555 1555 2.32 LINK CA CA A 304 O HOH A1132 1555 1555 2.50 LINK CA CA A 304 O HOH A1183 1555 1555 2.47 LINK CA CA A 305 O HOH A1003 1555 1555 2.53 LINK CA CA A 305 O HOH A1007 1555 1555 2.56 LINK CA CA A 305 O HOH A1020 1555 1555 2.50 LINK CA CA A 305 O HOH A1187 1555 1555 2.26 LINK OD2 ASP B 128 CA CA B 303 1555 1555 2.40 LINK O ASP B 162 CA CA B 304 1555 1555 2.28 LINK NE2 HIS B 172 ZN ZN B 301 1555 1555 1.96 LINK OD2 ASP B 174 ZN ZN B 301 1555 1555 2.01 LINK OD1 ASP B 179 CA CA B 302 1555 1555 2.31 LINK O GLY B 180 CA CA B 302 1555 1555 2.27 LINK O SER B 182 CA CA B 302 1555 1555 2.36 LINK O LEU B 184 CA CA B 302 1555 1555 2.29 LINK NE2 HIS B 187 ZN ZN B 301 1555 1555 2.05 LINK O ASN B 194 CA CA B 304 1555 1555 2.36 LINK O GLY B 196 CA CA B 304 1555 1555 2.30 LINK OD1 ASP B 198 CA CA B 304 1555 1555 2.41 LINK ND1 HIS B 200 ZN ZN B 301 1555 1555 2.03 LINK OD2 ASP B 202 CA CA B 302 1555 1555 2.33 LINK O ASP B 203 CA CA B 303 1555 1555 2.41 LINK OD2 ASP B 203 CA CA B 303 1555 1555 2.42 LINK OE2 GLU B 205 CA CA B 302 1555 1555 2.23 LINK O GLU B 205 CA CA B 303 1555 1555 2.29 LINK NE2 HIS B 222 ZN ZN B 300 1555 1555 2.07 LINK NE2 HIS B 226 ZN ZN B 300 1555 1555 2.07 LINK NE2 HIS B 232 ZN ZN B 300 1555 1555 2.09 LINK ZN ZN B 300 O21 24F B 400 1555 1555 1.91 LINK CA CA B 303 O HOH B1143 1555 1555 2.17 LINK CA CA B 303 O HOH B1201 1555 1555 2.99 LINK CA CA B 304 O HOH B1185 1555 1555 2.42 LINK CA CA B 304 O HOH B1186 1555 1555 2.34 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 24F A 400 SITE 1 AC2 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC3 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC3 6 ASP A 202 GLU A 205 SITE 1 AC4 4 ASP A 128 ASP A 203 GLU A 205 HOH A1184 SITE 1 AC5 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC5 6 HOH A1132 HOH A1183 SITE 1 AC6 6 SER A 146 THR A 149 HOH A1003 HOH A1007 SITE 2 AC6 6 HOH A1020 HOH A1187 SITE 1 AC7 18 TYR A 176 LEU A 184 LEU A 185 ALA A 186 SITE 2 AC7 18 HIS A 187 ALA A 188 LEU A 218 HIS A 222 SITE 3 AC7 18 GLU A 223 HIS A 226 HIS A 232 LEU A 239 SITE 4 AC7 18 PHE A 241 PRO A 242 ILE A 243 TYR A 244 SITE 5 AC7 18 ZN A 300 HOH A1202 SITE 1 AC8 4 HIS B 222 HIS B 226 HIS B 232 24F B 400 SITE 1 AC9 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 BC1 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 BC1 6 ASP B 202 GLU B 205 SITE 1 BC2 5 ASP B 128 ASP B 203 GLU B 205 HOH B1143 SITE 2 BC2 5 HOH B1201 SITE 1 BC3 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 BC3 6 HOH B1185 HOH B1186 SITE 1 BC4 15 LEU B 184 LEU B 185 ALA B 186 PHE B 189 SITE 2 BC4 15 LEU B 218 HIS B 222 GLU B 223 HIS B 226 SITE 3 BC4 15 HIS B 232 LEU B 239 PHE B 241 PRO B 242 SITE 4 BC4 15 ILE B 243 ZN B 300 HOH B1108 CRYST1 134.500 36.070 95.180 90.00 130.53 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 0.007435 0.000000 0.006357 0.00000 SCALE2 0.000000 0.027724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013823 0.00000