HEADER HYDROLASE/HYDROLASE INHIBITOR 27-MAY-15 5BPA TITLE X-RAY CO-STRUCTURE OF MMP-13 WITH 4-[({5-[2-(ETHOXYCARBONYL)-1H-INDOL- TITLE 2 5-YL]-1-METHYL-1H-PYRAZOL-3-YL}FORMAMIDO)METHYL]BENZOATE 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 FRAGMENT: 104-274; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 GENE: MMP13; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RIDGEFIELD, PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.A.FARROW,S.M.MARGARIT REVDAT 4 06-MAR-24 5BPA 1 REMARK LINK REVDAT 3 20-JUL-16 5BPA 1 REMARK REVDAT 2 07-OCT-15 5BPA 1 REMARK REVDAT 1 17-JUN-15 5BPA 0 JRNL AUTH S.J.TAYLOR,A.ABEYWARDANE,S.LIANG,I.MUEGGE,A.K.PADYANA, JRNL AUTH 2 Z.XIONG,M.HILL-DRZEWI,B.FARMER,X.LI,B.COLLINS,J.X.LI, JRNL AUTH 3 A.HEIM-RIETHER,J.PROUDFOOT,Q.ZHANG,D.GOLDBERG, JRNL AUTH 4 L.ZUVELA-JELASKA,H.ZAHER,J.LI,N.A.FARROW JRNL TITL FRAGMENT-BASED DISCOVERY OF INDOLE INHIBITORS OF MATRIX JRNL TITL 2 METALLOPROTEINASE-13. JRNL REF J. MED. CHEM. V. 54 8174 2011 JRNL REFN ISSN 1520-4804 JRNL PMID 22017539 JRNL DOI 10.1021/JM201129M REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 33138 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1657 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 67.5851 - 4.0978 0.99 2728 144 0.1641 0.1789 REMARK 3 2 4.0978 - 3.2526 0.99 2649 139 0.1555 0.1931 REMARK 3 3 3.2526 - 2.8414 0.99 2626 139 0.1798 0.2047 REMARK 3 4 2.8414 - 2.5816 1.00 2616 137 0.1800 0.2433 REMARK 3 5 2.5816 - 2.3966 1.00 2615 138 0.1849 0.2428 REMARK 3 6 2.3966 - 2.2553 1.00 2587 136 0.1939 0.2489 REMARK 3 7 2.2553 - 2.1423 0.99 2638 139 0.1906 0.2272 REMARK 3 8 2.1423 - 2.0491 1.00 2611 137 0.2046 0.2654 REMARK 3 9 2.0491 - 1.9702 0.99 2611 138 0.2120 0.2498 REMARK 3 10 1.9702 - 1.9022 1.00 2575 135 0.2314 0.3011 REMARK 3 11 1.9022 - 1.8427 1.00 2605 137 0.2456 0.3092 REMARK 3 12 1.8427 - 1.7900 1.00 2620 138 0.2681 0.3319 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 : 0.35 REMARK 3 B_SOL : 70.87 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.006 2852 REMARK 3 ANGLE : 0.945 3886 REMARK 3 CHIRALITY : 0.066 379 REMARK 3 PLANARITY : 0.005 508 REMARK 3 DIHEDRAL : 19.442 978 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 5BPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 67.537 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.96200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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 (%): 46.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG4000, 1M AMMONIUM FORMATE, 100 REMARK 280 MM TRIS, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 293K 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 67.64050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.07050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.64050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.07050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 3070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -133.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 531 LIES ON A SPECIAL POSITION. 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 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: 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 -131.76 47.40 REMARK 500 SER A 182 -175.35 68.72 REMARK 500 ASN A 194 -118.62 59.34 REMARK 500 SER A 210 -134.23 -116.26 REMARK 500 PRO A 242 32.94 -80.99 REMARK 500 LYS B 170 -128.89 44.95 REMARK 500 TYR B 176 73.51 -117.03 REMARK 500 SER B 182 178.91 74.50 REMARK 500 ASN B 194 -125.75 66.99 REMARK 500 SER B 210 -121.01 -120.32 REMARK 500 PRO B 242 33.74 -76.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 533 DISTANCE = 6.12 ANGSTROMS 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 OD1 REMARK 620 2 ASP A 128 OD2 42.5 REMARK 620 3 ASP A 203 O 166.5 149.3 REMARK 620 4 ASP A 203 OD2 119.5 104.8 68.9 REMARK 620 5 GLU A 205 O 105.3 68.6 82.5 99.3 REMARK 620 6 HOH B 488 O 88.3 121.0 78.5 131.3 111.4 REMARK 620 N 1 2 3 4 5 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 159.0 REMARK 620 3 GLY A 196 O 80.0 95.4 REMARK 620 4 ASP A 198 OD1 87.9 113.1 98.0 REMARK 620 5 HOH A 416 O 100.2 79.4 166.1 95.9 REMARK 620 N 1 2 3 4 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 109.2 REMARK 620 3 HIS A 187 NE2 114.5 114.7 REMARK 620 4 HIS A 200 ND1 106.2 98.3 112.5 REMARK 620 N 1 2 3 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 179 OD1 REMARK 620 2 GLY A 180 O 88.8 REMARK 620 3 SER A 182 O 87.4 85.1 REMARK 620 4 LEU A 184 O 92.1 178.4 93.7 REMARK 620 5 ASP A 202 OD2 96.0 90.5 174.3 90.7 REMARK 620 6 GLU A 205 OE2 167.4 86.7 80.5 92.1 95.8 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 98.4 REMARK 620 3 HIS A 232 NE2 117.9 99.6 REMARK 620 N 1 2 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 HOH A 501 O REMARK 620 2 ASP B 128 OD2 114.7 REMARK 620 3 ASP B 203 O 86.9 155.1 REMARK 620 4 ASP B 203 OD2 120.4 106.0 69.8 REMARK 620 5 GLU B 205 O 134.1 71.1 85.1 98.7 REMARK 620 N 1 2 3 4 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 163.8 REMARK 620 3 GLY B 196 O 76.1 94.6 REMARK 620 4 ASP B 198 OD1 89.4 104.2 90.6 REMARK 620 N 1 2 3 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 114.5 REMARK 620 3 HIS B 187 NE2 112.8 112.0 REMARK 620 4 HIS B 200 ND1 111.0 95.0 110.2 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 179 OD1 REMARK 620 2 GLY B 180 O 88.2 REMARK 620 3 SER B 182 O 78.3 85.6 REMARK 620 4 LEU B 184 O 98.2 173.5 96.2 REMARK 620 5 ASP B 202 OD2 97.7 87.7 172.3 90.8 REMARK 620 6 GLU B 205 OE1 153.5 93.3 75.4 81.2 108.9 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 103.7 REMARK 620 3 HIS B 232 NE2 115.9 95.8 REMARK 620 N 1 2 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 4UF 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 4UF B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BOY RELATED DB: PDB DBREF 5BPA A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 5BPA 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 301 1 HET ZN A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HET 4UF A 306 33 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 4UF B 306 33 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM 4UF 4-{[({5-[2-(ETHOXYCARBONYL)-1H-INDOL-5-YL]-1-METHYL-1H- HETNAM 2 4UF PYRAZOL-3-YL}CARBONYL)AMINO]METHYL}BENZOIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 4UF 2(C24 H22 N4 O5) FORMUL 15 HOH *277(H2 O) HELIX 1 AA1 THR A 130 ASP A 147 1 18 HELIX 2 AA2 LEU A 216 GLY A 229 1 14 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 LEU B 228 1 13 HELIX 6 AA6 PRO B 255 GLY B 267 1 13 SHEET 1 AA1 5 ASN A 152 LEU A 156 0 SHEET 2 AA1 5 ASN A 117 ILE A 122 1 N TYR A 120 O LEU A 156 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 303 1555 1555 3.13 LINK OD2 ASP A 128 CA CA A 303 1555 1555 2.92 LINK O ASP A 162 CA CA A 305 1555 1555 2.61 LINK NE2 HIS A 172 ZN ZN A 302 1555 1555 2.13 LINK OD2 ASP A 174 ZN ZN A 302 1555 1555 1.87 LINK OD1 ASP A 179 CA CA A 304 1555 1555 2.38 LINK O GLY A 180 CA CA A 304 1555 1555 2.29 LINK O SER A 182 CA CA A 304 1555 1555 2.38 LINK O LEU A 184 CA CA A 304 1555 1555 2.41 LINK NE2 HIS A 187 ZN ZN A 302 1555 1555 2.14 LINK O ASN A 194 CA CA A 305 1555 1555 2.46 LINK O GLY A 196 CA CA A 305 1555 1555 2.50 LINK OD1 ASP A 198 CA CA A 305 1555 1555 2.65 LINK ND1 HIS A 200 ZN ZN A 302 1555 1555 2.16 LINK OD2 ASP A 202 CA CA A 304 1555 1555 2.36 LINK O ASP A 203 CA CA A 303 1555 1555 2.88 LINK OD2 ASP A 203 CA CA A 303 1555 1555 2.92 LINK O GLU A 205 CA CA A 303 1555 1555 2.89 LINK OE2 GLU A 205 CA CA A 304 1555 1555 2.33 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 1.97 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.16 LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.16 LINK CA CA A 303 O HOH B 488 1555 2657 3.01 LINK CA CA A 305 O HOH A 416 1555 1555 2.77 LINK O HOH A 501 CA CA B 303 2657 1555 2.71 LINK OD2 ASP B 128 CA CA B 303 1555 1555 2.76 LINK O ASP B 162 CA CA B 305 1555 1555 2.63 LINK NE2 HIS B 172 ZN ZN B 302 1555 1555 2.07 LINK OD2 ASP B 174 ZN ZN B 302 1555 1555 2.02 LINK OD1 ASP B 179 CA CA B 304 1555 1555 2.48 LINK O GLY B 180 CA CA B 304 1555 1555 2.34 LINK O SER B 182 CA CA B 304 1555 1555 2.48 LINK O LEU B 184 CA CA B 304 1555 1555 2.32 LINK NE2 HIS B 187 ZN ZN B 302 1555 1555 2.14 LINK O ASN B 194 CA CA B 305 1555 1555 2.63 LINK O GLY B 196 CA CA B 305 1555 1555 2.64 LINK OD1 ASP B 198 CA CA B 305 1555 1555 2.66 LINK ND1 HIS B 200 ZN ZN B 302 1555 1555 2.06 LINK OD2 ASP B 202 CA CA B 304 1555 1555 2.40 LINK O ASP B 203 CA CA B 303 1555 1555 2.87 LINK OD2 ASP B 203 CA CA B 303 1555 1555 2.96 LINK O GLU B 205 CA CA B 303 1555 1555 2.83 LINK OE1 GLU B 205 CA CA B 304 1555 1555 2.53 LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 2.09 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.19 LINK NE2 HIS B 232 ZN ZN B 301 1555 1555 2.00 SITE 1 AC1 3 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 ASP A 128 ASP A 203 GLU A 205 HOH B 488 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 5 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC5 5 HOH A 416 SITE 1 AC6 20 LYS A 140 LEU A 185 ASN A 215 PHE A 217 SITE 2 AC6 20 LEU A 218 HIS A 222 GLU A 223 ALA A 238 SITE 3 AC6 20 LEU A 239 PHE A 241 PRO A 242 ILE A 243 SITE 4 AC6 20 THR A 245 TYR A 246 THR A 247 LYS A 249 SITE 5 AC6 20 PHE A 252 HOH A 410 HOH A 429 HOH A 474 SITE 1 AC7 3 HIS B 222 HIS B 226 HIS B 232 SITE 1 AC8 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC9 4 HOH A 501 ASP B 128 ASP B 203 GLU B 205 SITE 1 AD1 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AD1 6 ASP B 202 GLU B 205 SITE 1 AD2 4 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 1 AD3 20 LYS B 140 ASN B 215 PHE B 217 LEU B 218 SITE 2 AD3 20 VAL B 219 HIS B 222 GLU B 223 ALA B 238 SITE 3 AD3 20 LEU B 239 PHE B 241 ILE B 243 THR B 245 SITE 4 AD3 20 TYR B 246 THR B 247 LYS B 249 SER B 250 SITE 5 AD3 20 HIS B 251 PHE B 252 HOH B 440 HOH B 446 CRYST1 135.281 36.141 96.097 90.00 131.48 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 0.007392 0.000000 0.006536 0.00000 SCALE2 0.000000 0.027669 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013891 0.00000