PDB Short entry for 5BOT HEADER HYDROLASE/HYDROLASE INHIBITOR 27-MAY-15 5BOT TITLE X-RAY CO-STRUCTURE OF MMP-13 WITH ETHYL 5-CARBAMOYL-1H-INDOLE-2- TITLE 2 CARBOXYLATE 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,A.K.PADYANA REVDAT 5 06-MAR-24 5BOT 1 LINK REVDAT 4 13-JUN-18 5BOT 1 REMARK REVDAT 3 27-JUL-16 5BOT 1 REMARK REVDAT 2 07-OCT-15 5BOT 1 REMARK REVDAT 1 17-JUN-15 5BOT 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. 1.85 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 28513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 1.9161 - 1.8500 0.00 0 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 5BOT 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_1000210090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 63 REMARK 200 PH : NULL 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 FR-E DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.6 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 : 28513 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.977 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 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: 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 (%): 46.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-28% PEG 4000 0.6M AMMONIUM FORMATE REMARK 280 0. M TRIS PH 8, VAPOR DIFFUSION, HANGING DROP, 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 67.32050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.97650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.32050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.97650 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: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -136.0 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 A 624 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 621 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 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 IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 HIS B 251 O HOH B 401 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 248 N - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 108 153.57 -43.82 REMARK 500 LEU A 111 104.20 -55.79 REMARK 500 LYS A 170 -130.62 48.04 REMARK 500 SER A 182 -179.04 71.16 REMARK 500 ASN A 194 -117.77 59.94 REMARK 500 SER A 210 -159.87 -130.74 REMARK 500 LYS B 170 -133.63 47.64 REMARK 500 TYR B 176 73.92 -111.80 REMARK 500 SER B 182 -179.71 73.74 REMARK 500 ASN B 194 -120.64 58.41 REMARK 500 SER B 210 -122.43 -120.50 REMARK 500 PRO B 242 39.34 -81.53 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 A 639 DISTANCE = 6.66 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 001 REMARK 600 MOL_POTENCY [IC50 IN NM] 65000 REMARK 600 CDB_METHOD_ID 18655 REMARK 600 BRD_ID REMARK 600 001 DICTIONARY 17 18 OTHER REMARK 600 001 C1 C1 C 0 YNN 1 REMARK 600 001 C2 C2 C 0 YNN 2 REMARK 600 001 C3 C3 C 0 YNN 3 REMARK 600 001 C4 C4 C 0 YNN 4 REMARK 600 001 N5 N5 N 0 YNN 5 REMARK 600 001 C6 C6 C 0 YNN 6 REMARK 600 001 C7 C7 C 0 YNN 7 REMARK 600 001 C8 C8 C 0 YNN 8 REMARK 600 001 C9 C9 C 0 YNN 9 REMARK 600 001 C10 C10 C 0 NNN 10 REMARK 600 001 C11 C11 C 0 NNN 11 REMARK 600 001 O12 O12 O 0 NNN 12 REMARK 600 001 O13 O13 O 0 NNN 13 REMARK 600 001 N14 N14 N 0 NNN 14 REMARK 600 001 O15 O15 O 0 NNN 15 REMARK 600 001 C16 C16 C 0 NNN 16 REMARK 600 001 C17 C17 C 0 NNN 17 REMARK 600 001 C1 C2 DOUB YN 1 REMARK 600 001 C1 C3 SING YN 2 REMARK 600 001 C1 C4 SING YN 3 REMARK 600 001 C2 N5 SING YN 4 REMARK 600 001 C2 C6 SING YN 5 REMARK 600 001 C3 C7 DOUB YN 6 REMARK 600 001 C4 C8 DOUB YN 7 REMARK 600 001 N5 C7 SING YN 8 REMARK 600 001 C6 C9 DOUB YN 9 REMARK 600 001 C7 C10 SING NN 10 REMARK 600 001 C8 C9 SING YN 11 REMARK 600 001 C8 C11 SING NN 12 REMARK 600 001 C10 O12 SING NN 13 REMARK 600 001 C10 O13 DOUB NN 14 REMARK 600 001 C11 N14 SING NN 15 REMARK 600 001 C11 O15 DOUB NN 16 REMARK 600 001 O12 C16 SING NN 17 REMARK 600 001 C16 C17 SING NN 18 REMARK 600 ZN2 DICTIONARY 1 0 OTHER REMARK 600 ZN2 ZN ZN ZN 2 NNN 1 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 45.5 REMARK 620 3 ASP A 203 O 155.1 157.6 REMARK 620 4 ASP A 203 OD2 109.7 95.9 70.4 REMARK 620 5 GLU A 205 O 111.3 75.4 91.5 107.5 REMARK 620 6 HOH A 534 O 91.0 104.5 87.4 157.8 70.3 REMARK 620 7 HOH A 564 O 76.7 122.2 79.2 103.8 142.0 72.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 170.3 REMARK 620 3 GLY A 196 O 93.0 95.8 REMARK 620 4 ASP A 198 OD1 87.3 97.0 87.4 REMARK 620 5 HOH A 409 O 89.5 81.3 172.7 99.6 REMARK 620 6 HOH A 491 O 86.2 90.5 85.5 170.1 87.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 110.3 REMARK 620 3 HIS A 187 NE2 114.1 114.9 REMARK 620 4 HIS A 200 ND1 110.7 93.2 111.8 REMARK 620 N 1 2 3 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 179 OD1 REMARK 620 2 GLY A 180 O 87.4 REMARK 620 3 SER A 182 O 85.3 85.7 REMARK 620 4 LEU A 184 O 95.2 177.3 93.9 REMARK 620 5 ASP A 202 OD2 91.5 88.9 173.8 91.6 REMARK 620 6 GLU A 205 OE2 167.6 90.1 82.4 87.2 100.5 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 222 NE2 REMARK 620 2 HIS A 226 NE2 95.6 REMARK 620 3 HIS A 232 NE2 108.8 98.1 REMARK 620 N 1 2 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 HOH A 418 O REMARK 620 2 HOH A 510 O 76.8 REMARK 620 3 ASP B 128 OD1 74.3 83.9 REMARK 620 4 ASP B 128 OD2 120.5 97.4 46.4 REMARK 620 5 ASP B 203 O 78.8 97.8 151.9 157.8 REMARK 620 6 ASP B 203 OD2 100.3 172.5 102.0 90.0 74.8 REMARK 620 7 GLU B 205 O 148.0 76.4 119.5 80.1 87.9 104.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 306 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 167.5 REMARK 620 3 GLY B 196 O 94.2 96.4 REMARK 620 4 ASP B 198 OD1 87.6 98.6 92.2 REMARK 620 5 HOH B 422 O 90.3 84.8 81.1 172.8 REMARK 620 6 HOH B 453 O 91.2 77.4 170.2 96.1 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 113.0 REMARK 620 3 HIS B 187 NE2 113.4 112.1 REMARK 620 4 HIS B 200 ND1 110.8 95.8 110.4 REMARK 620 N 1 2 3 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 179 OD1 REMARK 620 2 GLY B 180 O 89.2 REMARK 620 3 SER B 182 O 84.4 84.4 REMARK 620 4 LEU B 184 O 92.4 178.4 95.6 REMARK 620 5 ASP B 202 OD2 93.3 88.6 172.6 91.5 REMARK 620 6 GLU B 205 OE1 167.3 91.7 83.1 86.8 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 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 102.4 REMARK 620 3 HIS B 232 NE2 114.0 99.3 REMARK 620 4 HOH B 532 O 116.7 106.8 114.8 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: MOE REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: MOE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4UM 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 ZN 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 CA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4UM 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 ZN 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 CA B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BOY RELATED DB: PDB REMARK 900 RELATED ID: 5BPA RELATED DB: PDB DBREF 5BOT A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 5BOT 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 4UM A 301 17 HET ZN A 302 1 HET ZN A 303 1 HET CA A 304 1 HET CA A 305 1 HET CA A 306 1 HET 4UM B 301 17 HET ZN B 302 1 HET ZN B 303 1 HET CA B 304 1 HET CA B 305 1 HET CA B 306 1 HETNAM 4UM ETHYL 5-CARBAMOYL-1H-INDOLE-2-CARBOXYLATE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 4UM 2(C12 H12 N2 O3) FORMUL 4 ZN 4(ZN 2+) FORMUL 6 CA 6(CA 2+) FORMUL 15 HOH *471(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 GLY B 229 1 14 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 SER A 166 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 2 LEU A 230 ASP A 231 0 SHEET 2 AA3 2 ASN B 105 VAL B 106 -1 O ASN B 105 N ASP A 231 SHEET 1 AA4 5 ASN B 152 ARG B 155 0 SHEET 2 AA4 5 ASN B 117 ILE B 122 1 N LEU B 118 O ASN B 152 SHEET 3 AA4 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121 SHEET 4 AA4 5 ALA B 199 ASP B 202 1 O PHE B 201 N SER B 166 SHEET 5 AA4 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200 SHEET 1 AA5 2 TRP B 207 THR B 208 0 SHEET 2 AA5 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 3.02 LINK OD2 ASP A 128 CA CA A 304 1555 1555 2.54 LINK O ASP A 162 CA CA A 306 1555 1555 2.39 LINK NE2 HIS A 172 ZN ZN A 303 1555 1555 2.11 LINK OD2 ASP A 174 ZN ZN A 303 1555 1555 2.00 LINK OD1 ASP A 179 CA CA A 305 1555 1555 2.41 LINK O GLY A 180 CA CA A 305 1555 1555 2.37 LINK O SER A 182 CA CA A 305 1555 1555 2.53 LINK O LEU A 184 CA CA A 305 1555 1555 2.37 LINK NE2 HIS A 187 ZN ZN A 303 1555 1555 2.12 LINK O ASN A 194 CA CA A 306 1555 1555 2.41 LINK O GLY A 196 CA CA A 306 1555 1555 2.31 LINK OD1 ASP A 198 CA CA A 306 1555 1555 2.47 LINK ND1 HIS A 200 ZN ZN A 303 1555 1555 2.14 LINK OD2 ASP A 202 CA CA A 305 1555 1555 2.37 LINK O ASP A 203 CA CA A 304 1555 1555 2.71 LINK OD2 ASP A 203 CA CA A 304 1555 1555 2.73 LINK O GLU A 205 CA CA A 304 1555 1555 2.50 LINK OE2 GLU A 205 CA CA A 305 1555 1555 2.32 LINK NE2 HIS A 222 ZN ZN A 302 1555 1555 2.19 LINK NE2 HIS A 226 ZN ZN A 302 1555 1555 2.10 LINK NE2 HIS A 232 ZN ZN A 302 1555 1555 2.10 LINK CA CA A 304 O HOH A 534 1555 1555 2.72 LINK CA CA A 304 O HOH A 564 1555 1555 2.64 LINK CA CA A 306 O HOH A 409 1555 1555 2.48 LINK CA CA A 306 O HOH A 491 1555 1555 2.43 LINK O HOH A 418 CA CA B 304 2657 1555 2.55 LINK O HOH A 510 CA CA B 304 2657 1555 2.60 LINK OD1 ASP B 128 CA CA B 304 1555 1555 2.98 LINK OD2 ASP B 128 CA CA B 304 1555 1555 2.52 LINK O ASP B 162 CA CA B 306 1555 1555 2.34 LINK NE2 HIS B 172 ZN ZN B 303 1555 1555 2.08 LINK OD2 ASP B 174 ZN ZN B 303 1555 1555 2.00 LINK OD1 ASP B 179 CA CA B 305 1555 1555 2.41 LINK O GLY B 180 CA CA B 305 1555 1555 2.37 LINK O SER B 182 CA CA B 305 1555 1555 2.51 LINK O LEU B 184 CA CA B 305 1555 1555 2.33 LINK NE2 HIS B 187 ZN ZN B 303 1555 1555 2.12 LINK O ASN B 194 CA CA B 306 1555 1555 2.41 LINK O GLY B 196 CA CA B 306 1555 1555 2.37 LINK OD1 ASP B 198 CA CA B 306 1555 1555 2.48 LINK ND1 HIS B 200 ZN ZN B 303 1555 1555 2.12 LINK OD2 ASP B 202 CA CA B 305 1555 1555 2.37 LINK O ASP B 203 CA CA B 304 1555 1555 2.58 LINK OD2 ASP B 203 CA CA B 304 1555 1555 2.56 LINK O GLU B 205 CA CA B 304 1555 1555 2.45 LINK OE1 GLU B 205 CA CA B 305 1555 1555 2.32 LINK NE2 HIS B 222 ZN ZN B 302 1555 1555 2.13 LINK NE2 HIS B 226 ZN ZN B 302 1555 1555 2.13 LINK NE2 HIS B 232 ZN ZN B 302 1555 1555 2.13 LINK ZN ZN B 302 O HOH B 532 1555 1555 2.19 LINK CA CA B 306 O HOH B 422 1555 1555 2.38 LINK CA CA B 306 O HOH B 453 1555 1555 2.46 SITE 1 AC1 11 HIS A 222 GLU A 223 ALA A 238 LEU A 239 SITE 2 AC1 11 PHE A 241 PRO A 242 ILE A 243 THR A 245 SITE 3 AC1 11 THR A 247 PHE A 252 HOH A 410 SITE 1 AC2 3 HIS A 222 HIS A 226 HIS A 232 SITE 1 AC3 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC4 5 ASP A 128 ASP A 203 GLU A 205 HOH A 534 SITE 2 AC4 5 HOH A 564 SITE 1 AC5 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC5 6 ASP A 202 GLU A 205 SITE 1 AC6 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC6 6 HOH A 409 HOH A 491 SITE 1 AC7 10 HIS B 222 ALA B 238 LEU B 239 PHE B 241 SITE 2 AC7 10 PRO B 242 ILE B 243 THR B 245 PHE B 252 SITE 3 AC7 10 HOH B 407 HOH B 501 SITE 1 AC8 4 HIS B 222 HIS B 226 HIS B 232 HOH B 532 SITE 1 AC9 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AD1 5 HOH A 418 HOH A 510 ASP B 128 ASP B 203 SITE 2 AD1 5 GLU B 205 SITE 1 AD2 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AD2 6 ASP B 202 GLU B 205 SITE 1 AD3 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 AD3 6 HOH B 422 HOH B 453 CRYST1 134.641 35.953 95.824 90.00 130.78 90.00 C 1 2 1 8 ORIGX1 0.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.000000 0.00000 SCALE1 0.007427 0.000000 0.006406 0.00000 SCALE2 0.000000 0.027814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013782 0.00000