PDB Short entry for 5UWK HEADER HYDROLASE/HYDROLASE INHIBITOR 21-FEB-17 5UWK TITLE MATRIX METALLOPROTEINASE-13 COMPLEXED WITH SELECTIVE INHIBITOR TITLE 2 COMPOUND (S)-10A COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MATRIX METALLOPROTEINASE-13,MMP-13; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CATALYTIC DOMAIN (UNP RESIDUES 104-274) 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKA8H KEYWDS METALLOPROTEINASE, COLLAGENASE, MMP-13, HYDROLASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.B.TAYLOR,X.CAO,P.J.HART REVDAT 3 04-OCT-23 5UWK 1 LINK REVDAT 2 26-JUL-17 5UWK 1 JRNL REVDAT 1 12-JUL-17 5UWK 0 JRNL AUTH J.Y.CHOI,R.FUERST,A.M.KNAPINSKA,A.B.TAYLOR,L.SMITH,X.CAO, JRNL AUTH 2 P.J.HART,G.B.FIELDS,W.R.ROUSH JRNL TITL STRUCTURE-BASED DESIGN AND SYNTHESIS OF POTENT AND SELECTIVE JRNL TITL 2 MATRIX METALLOPROTEINASE 13 INHIBITORS. JRNL REF J. MED. CHEM. V. 60 5816 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28653849 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00514 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 42432 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 51.6725 - 3.8557 0.97 3006 149 0.1379 0.1515 REMARK 3 2 3.8557 - 3.0605 0.99 2949 146 0.1349 0.1953 REMARK 3 3 3.0605 - 2.6737 1.00 2928 144 0.1645 0.2205 REMARK 3 4 2.6737 - 2.4292 1.00 2903 145 0.1562 0.1898 REMARK 3 5 2.4292 - 2.2551 1.00 2906 143 0.1426 0.1821 REMARK 3 6 2.2551 - 2.1221 1.00 2874 142 0.1373 0.1889 REMARK 3 7 2.1221 - 2.0159 1.00 2861 141 0.1307 0.1931 REMARK 3 8 2.0159 - 1.9281 1.00 2859 141 0.1412 0.2273 REMARK 3 9 1.9281 - 1.8539 1.00 2882 143 0.1535 0.2425 REMARK 3 10 1.8539 - 1.7899 1.00 2849 141 0.1517 0.2299 REMARK 3 11 1.7899 - 1.7339 1.00 2868 142 0.1621 0.2320 REMARK 3 12 1.7339 - 1.6844 1.00 2846 141 0.1833 0.2740 REMARK 3 13 1.6844 - 1.6400 1.00 2846 140 0.1955 0.2957 REMARK 3 14 1.6400 - 1.6000 1.00 2855 142 0.2047 0.2877 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 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 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 : 0.008 2724 REMARK 3 ANGLE : 1.101 3708 REMARK 3 CHIRALITY : 0.052 368 REMARK 3 PLANARITY : 0.007 476 REMARK 3 DIHEDRAL : 16.023 954 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 5UWK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42491 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 120.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.76800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4L19 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M REMARK 280 TRIS:HCL PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K 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 22.89200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.28200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.57750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.28200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.89200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.57750 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: 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 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 MET A 103 REMARK 465 TYR A 104 REMARK 465 ASN A 105 REMARK 465 VAL A 106 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 HIS A 251 REMARK 465 ASP A 270 REMARK 465 GLU A 271 REMARK 465 ASP A 272 REMARK 465 PRO A 273 REMARK 465 ASN A 274 REMARK 465 MET B 103 REMARK 465 TYR B 104 REMARK 465 ASN B 105 REMARK 465 VAL B 106 REMARK 465 LYS B 249 REMARK 465 SER B 250 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 111 149.13 -175.32 REMARK 500 LYS A 170 -131.16 44.71 REMARK 500 SER A 182 -174.26 76.88 REMARK 500 ASN A 194 -121.82 62.21 REMARK 500 PRO B 108 73.37 -106.65 REMARK 500 LYS B 170 -133.52 46.39 REMARK 500 TYR B 176 77.66 -111.45 REMARK 500 SER B 182 -175.03 66.68 REMARK 500 ASN B 194 -119.16 60.81 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 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD1 REMARK 620 2 ASP A 128 OD2 49.5 REMARK 620 3 ASP A 203 O 148.4 158.6 REMARK 620 4 ASP A 203 OD1 92.0 97.8 74.3 REMARK 620 5 GLU A 205 O 128.1 81.5 83.5 113.4 REMARK 620 6 HOH A 427 O 82.8 132.0 66.6 77.3 144.7 REMARK 620 7 HOH A 512 O 87.6 94.6 97.6 163.5 79.3 86.3 REMARK 620 N 1 2 3 4 5 6 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 ASP A 162 O REMARK 620 2 ASN A 194 O 168.4 REMARK 620 3 GLY A 196 O 93.6 97.1 REMARK 620 4 ASP A 198 OD1 86.0 98.1 92.0 REMARK 620 5 HOH A 416 O 85.8 82.8 170.9 97.1 REMARK 620 6 HOH A 466 O 87.5 89.2 83.9 172.0 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 111.1 REMARK 620 3 HIS A 187 NE2 115.6 114.9 REMARK 620 4 HIS A 200 ND1 104.0 96.9 112.3 REMARK 620 N 1 2 3 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 179 OD1 REMARK 620 2 GLY A 180 O 88.7 REMARK 620 3 SER A 182 O 85.1 87.2 REMARK 620 4 LEU A 184 O 96.1 173.1 88.3 REMARK 620 5 ASP A 202 OD2 94.5 96.0 176.8 88.6 REMARK 620 6 GLU A 205 OE2 166.2 86.4 81.8 87.8 98.7 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 222 NE2 REMARK 620 2 HIS A 226 NE2 104.2 REMARK 620 3 HIS A 232 NE2 111.1 102.0 REMARK 620 4 8OM A 306 O2 119.5 121.6 96.5 REMARK 620 N 1 2 3 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 128 OD1 REMARK 620 2 ASP B 128 OD2 47.5 REMARK 620 3 ASP B 203 O 146.0 160.4 REMARK 620 4 ASP B 203 OD1 95.0 93.5 73.5 REMARK 620 5 GLU B 205 O 126.6 82.8 87.3 108.0 REMARK 620 6 HOH B 424 O 80.7 127.2 65.8 79.3 149.4 REMARK 620 7 HOH B 523 O 85.8 97.3 98.1 165.9 82.4 87.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 167.6 REMARK 620 3 GLY B 196 O 91.8 99.7 REMARK 620 4 ASP B 198 OD1 87.0 97.8 88.9 REMARK 620 5 HOH B 415 O 84.2 83.7 170.2 99.8 REMARK 620 6 HOH B 458 O 88.9 88.1 81.6 169.5 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 109.5 REMARK 620 3 HIS B 187 NE2 117.6 117.6 REMARK 620 4 HIS B 200 ND1 103.5 93.6 111.5 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 179 OD1 REMARK 620 2 GLY B 180 O 90.8 REMARK 620 3 SER B 182 O 86.1 89.1 REMARK 620 4 LEU B 184 O 98.9 170.1 89.4 REMARK 620 5 ASP B 202 OD2 92.5 92.1 178.2 89.6 REMARK 620 6 GLU B 205 OE2 167.5 85.4 82.0 84.7 99.4 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 222 NE2 REMARK 620 2 HIS B 226 NE2 102.0 REMARK 620 3 HIS B 232 NE2 113.4 100.7 REMARK 620 4 8OM B 306 O2 119.3 121.5 98.8 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8OM A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8OM B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UWL RELATED DB: PDB REMARK 900 RELATED ID: 5UWM RELATED DB: PDB REMARK 900 RELATED ID: 5UWN RELATED DB: PDB DBREF 5UWK A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 5UWK B 104 274 UNP P45452 MMP13_HUMAN 104 274 SEQADV 5UWK MET A 103 UNP P45452 INITIATING METHIONINE SEQADV 5UWK MET B 103 UNP P45452 INITIATING METHIONINE SEQRES 1 A 172 MET TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS SEQRES 2 A 172 MET ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP SEQRES 3 A 172 MET THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA SEQRES 4 A 172 PHE LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR SEQRES 5 A 172 ARG LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE SEQRES 6 A 172 GLY ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY SEQRES 7 A 172 PRO SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO SEQRES 8 A 172 ASN TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR SEQRES 9 A 172 TRP THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL SEQRES 10 A 172 ALA ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SEQRES 11 A 172 SER LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR SEQRES 12 A 172 TYR THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP SEQRES 13 A 172 VAL GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU SEQRES 14 A 172 ASP PRO ASN SEQRES 1 B 172 MET TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS SEQRES 2 B 172 MET ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP SEQRES 3 B 172 MET THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA SEQRES 4 B 172 PHE LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR SEQRES 5 B 172 ARG LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE SEQRES 6 B 172 GLY ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY SEQRES 7 B 172 PRO SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO SEQRES 8 B 172 ASN TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR SEQRES 9 B 172 TRP THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL SEQRES 10 B 172 ALA ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SEQRES 11 B 172 SER LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR SEQRES 12 B 172 TYR THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP SEQRES 13 B 172 VAL GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU SEQRES 14 B 172 ASP PRO ASN HET ZN A 301 1 HET ZN A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HET 8OM A 306 35 HET ZN B 301 1 HET ZN B 302 1 HET CA B 303 1 HET CA B 304 1 HET CA B 305 1 HET 8OM B 306 35 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM 8OM (S)-3-METHYL-2-(4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H- HETNAM 2 8OM CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'- HETNAM 3 8OM BIPHENYL]-4-YLSULFONAMIDO)BUTANOIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 8OM 2(C25 H27 N3 O5 S2) FORMUL 15 HOH *364(H2 O) HELIX 1 AA1 THR A 130 ASP A 147 1 18 HELIX 2 AA2 LEU A 216 LEU A 228 1 13 HELIX 3 AA3 PRO A 255 GLY A 267 1 13 HELIX 4 AA4 THR B 130 ASP B 147 1 18 HELIX 5 AA5 LEU B 216 GLY B 229 1 14 HELIX 6 AA6 PRO B 255 GLY B 267 1 13 SHEET 1 AA1 5 ASN A 152 ARG A 155 0 SHEET 2 AA1 5 ASN A 117 ILE A 122 1 N LEU A 118 O ASN A 152 SHEET 3 AA1 5 ILE A 163 GLY A 168 1 O ILE A 165 N ARG A 121 SHEET 4 AA1 5 ALA A 199 ASP A 202 1 O PHE A 201 N GLY A 168 SHEET 5 AA1 5 ALA A 186 ALA A 188 -1 N HIS A 187 O HIS A 200 SHEET 1 AA2 2 TRP A 207 THR A 208 0 SHEET 2 AA2 2 TYR A 214 ASN A 215 1 O TYR A 214 N THR A 208 SHEET 1 AA3 5 ASN B 152 ARG B 155 0 SHEET 2 AA3 5 ASN B 117 ILE B 122 1 N LEU B 118 O ASN B 152 SHEET 3 AA3 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121 SHEET 4 AA3 5 ALA B 199 ASP B 202 1 O PHE B 201 N GLY B 168 SHEET 5 AA3 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200 SHEET 1 AA4 2 TRP B 207 THR B 208 0 SHEET 2 AA4 2 TYR B 214 ASN B 215 1 O TYR B 214 N THR B 208 LINK OD1 ASP A 128 CA CA A 304 1555 1555 2.77 LINK OD2 ASP A 128 CA CA A 304 1555 1555 2.43 LINK O ASP A 162 CA CA A 305 1555 1555 2.37 LINK NE2 HIS A 172 ZN ZN A 302 1555 1555 2.06 LINK OD2 ASP A 174 ZN ZN A 302 1555 1555 2.03 LINK OD1 ASP A 179 CA CA A 303 1555 1555 2.36 LINK O GLY A 180 CA CA A 303 1555 1555 2.19 LINK O SER A 182 CA CA A 303 1555 1555 2.37 LINK O LEU A 184 CA CA A 303 1555 1555 2.33 LINK NE2 HIS A 187 ZN ZN A 302 1555 1555 2.11 LINK O ASN A 194 CA CA A 305 1555 1555 2.34 LINK O GLY A 196 CA CA A 305 1555 1555 2.25 LINK OD1 ASP A 198 CA CA A 305 1555 1555 2.38 LINK ND1 HIS A 200 ZN ZN A 302 1555 1555 2.04 LINK OD2 ASP A 202 CA CA A 303 1555 1555 2.33 LINK O ASP A 203 CA CA A 304 1555 1555 2.61 LINK OD1 ASP A 203 CA CA A 304 1555 1555 2.39 LINK OE2 GLU A 205 CA CA A 303 1555 1555 2.20 LINK O GLU A 205 CA CA A 304 1555 1555 2.44 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.07 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.05 LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.00 LINK ZN ZN A 301 O2 8OM A 306 1555 1555 1.96 LINK CA CA A 304 O HOH A 427 1555 1555 2.25 LINK CA CA A 304 O HOH A 512 1555 1555 2.34 LINK CA CA A 305 O HOH A 416 1555 1555 2.42 LINK CA CA A 305 O HOH A 466 1555 1555 2.32 LINK OD1 ASP B 128 CA CA B 304 1555 1555 2.91 LINK OD2 ASP B 128 CA CA B 304 1555 1555 2.49 LINK O ASP B 162 CA CA B 305 1555 1555 2.34 LINK NE2 HIS B 172 ZN ZN B 302 1555 1555 2.02 LINK OD2 ASP B 174 ZN ZN B 302 1555 1555 1.92 LINK OD1 ASP B 179 CA CA B 303 1555 1555 2.37 LINK O GLY B 180 CA CA B 303 1555 1555 2.26 LINK O SER B 182 CA CA B 303 1555 1555 2.44 LINK O LEU B 184 CA CA B 303 1555 1555 2.35 LINK NE2 HIS B 187 ZN ZN B 302 1555 1555 2.07 LINK O ASN B 194 CA CA B 305 1555 1555 2.31 LINK O GLY B 196 CA CA B 305 1555 1555 2.35 LINK OD1 ASP B 198 CA CA B 305 1555 1555 2.36 LINK ND1 HIS B 200 ZN ZN B 302 1555 1555 2.04 LINK OD2 ASP B 202 CA CA B 303 1555 1555 2.35 LINK O ASP B 203 CA CA B 304 1555 1555 2.65 LINK OD1 ASP B 203 CA CA B 304 1555 1555 2.51 LINK OE2 GLU B 205 CA CA B 303 1555 1555 2.33 LINK O GLU B 205 CA CA B 304 1555 1555 2.44 LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 1.98 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.08 LINK NE2 HIS B 232 ZN ZN B 301 1555 1555 2.02 LINK ZN ZN B 301 O2 8OM B 306 1555 1555 1.96 LINK CA CA B 304 O HOH B 424 1555 1555 2.22 LINK CA CA B 304 O HOH B 523 1555 1555 2.31 LINK CA CA B 305 O HOH B 415 1555 1555 2.42 LINK CA CA B 305 O HOH B 458 1555 1555 2.28 CISPEP 1 PHE A 107 PRO A 108 0 -10.36 CISPEP 2 PHE B 107 PRO B 108 0 14.06 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 8OM A 306 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 5 ASP A 128 ASP A 203 GLU A 205 HOH A 427 SITE 2 AC4 5 HOH A 512 SITE 1 AC5 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC5 6 HOH A 416 HOH A 466 SITE 1 AC6 22 LEU A 184 LEU A 185 ALA A 186 LEU A 218 SITE 2 AC6 22 HIS A 222 GLU A 223 HIS A 226 HIS A 232 SITE 3 AC6 22 GLY A 237 LEU A 239 PHE A 241 PRO A 242 SITE 4 AC6 22 ILE A 243 TYR A 244 THR A 245 THR A 247 SITE 5 AC6 22 PHE A 252 PRO A 255 ZN A 301 HOH A 460 SITE 6 AC6 22 HOH A 493 HOH A 517 SITE 1 AC7 4 HIS B 222 HIS B 226 HIS B 232 8OM B 306 SITE 1 AC8 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC9 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AC9 6 ASP B 202 GLU B 205 SITE 1 AD1 5 ASP B 128 ASP B 203 GLU B 205 HOH B 424 SITE 2 AD1 5 HOH B 523 SITE 1 AD2 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 AD2 6 HOH B 415 HOH B 458 SITE 1 AD3 19 PHE A 107 LEU B 184 LEU B 185 ALA B 186 SITE 2 AD3 19 LEU B 218 HIS B 222 GLU B 223 HIS B 226 SITE 3 AD3 19 HIS B 232 LEU B 239 PHE B 241 PRO B 242 SITE 4 AD3 19 ILE B 243 TYR B 244 THR B 245 THR B 247 SITE 5 AD3 19 ZN B 301 HOH B 450 HOH B 497 CRYST1 45.784 57.155 120.564 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 0.021842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008294 0.00000