HEADER HYDROLASE 29-AUG-05 2D1N TITLE COLLAGENASE-3 (MMP-13) COMPLEXED TO A HYDROXAMIC ACID INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL CATALYTIC DOMAIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDOROLASE METALLOPROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KOHNO,H.HOCHIGAI,E.YAMASHITA,T.TSUKIHARA,M.KANAOKA REVDAT 5 25-OCT-23 2D1N 1 REMARK HETSYN LINK REVDAT 4 18-JUL-18 2D1N 1 REMARK REVDAT 3 13-JUL-11 2D1N 1 VERSN REVDAT 2 24-FEB-09 2D1N 1 VERSN REVDAT 1 27-JUN-06 2D1N 0 JRNL AUTH T.KOHNO,H.HOCHIGAI,E.YAMASHITA,T.TSUKIHARA,M.KANAOKA JRNL TITL CRYSTAL STRUCTURES OF THE CATALYTIC DOMAIN OF HUMAN JRNL TITL 2 STROMELYSIN-1 (MMP-3) AND COLLAGENASE-3 (MMP-13) WITH A JRNL TITL 3 HYDROXAMIC ACID INHIBITOR SM-25453 JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 344 315 2006 JRNL REFN ISSN 0006-291X JRNL PMID 16603129 JRNL DOI 10.1016/J.BBRC.2006.03.098 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1380522.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 27420 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 SET) : 0.218 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2728 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3909 REMARK 3 BIN R VALUE (WORKING SET) : 0.3750 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 391 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2644 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.72000 REMARK 3 B22 (A**2) : -5.72000 REMARK 3 B33 (A**2) : 11.44000 REMARK 3 B12 (A**2) : 2.61000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.50 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.52 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.47 REMARK 3 BSOL : 65.15 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 : FA2.PARAM 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 : FA2.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27785 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 830C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE, HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.01333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.50667 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: PQS 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: PQS 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 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 -124.06 49.53 REMARK 500 SER A 182 -169.55 64.72 REMARK 500 ASN A 194 -119.77 58.68 REMARK 500 PRO A 236 -9.74 -59.53 REMARK 500 PRO A 242 27.68 -59.92 REMARK 500 LYS B 170 -125.13 48.70 REMARK 500 SER B 182 -165.25 60.49 REMARK 500 ASN B 194 -120.95 57.37 REMARK 500 PRO B 236 -9.14 -59.60 REMARK 500 PRO B 242 32.97 -61.46 REMARK 500 HIS B 251 74.53 63.06 REMARK 500 PRO B 268 -170.86 -67.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 285 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 7 O REMARK 620 2 GLU A 135 OE1 154.8 REMARK 620 3 HIS B 157 NE2 100.2 101.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 286 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 8 O REMARK 620 2 HIS A 157 NE2 124.8 REMARK 620 3 GLU B 135 OE1 118.2 112.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 273 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 11 O REMARK 620 2 HOH A 41 O 88.6 REMARK 620 3 ASP A 162 O 71.4 90.5 REMARK 620 4 ASN A 194 O 91.4 77.7 159.6 REMARK 620 5 GLY A 196 O 79.8 168.4 85.2 103.1 REMARK 620 6 ASP A 198 OD1 166.0 98.8 96.5 101.7 92.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 274 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 128 OD1 41.5 REMARK 620 3 ASP A 203 OD2 106.3 104.6 REMARK 620 4 ASP A 203 O 173.6 144.0 76.4 REMARK 620 5 GLU A 205 O 82.3 114.7 125.0 91.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 271 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 111.2 REMARK 620 3 HIS A 187 NE2 109.3 116.1 REMARK 620 4 HIS A 200 ND1 108.5 90.8 119.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 272 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 89.2 REMARK 620 3 SER A 182 O 77.1 89.3 REMARK 620 4 LEU A 184 O 97.3 173.4 92.8 REMARK 620 5 ASP A 202 OD2 107.7 84.1 171.8 93.1 REMARK 620 6 GLU A 205 OE2 160.9 82.2 85.7 91.8 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 270 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 100.2 REMARK 620 3 HIS A 232 NE2 103.1 100.4 REMARK 620 4 FA4 A1001 O32 83.0 108.4 149.1 REMARK 620 5 FA4 A1001 O33 147.6 109.2 85.2 75.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 283 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 18 O REMARK 620 2 HOH B 19 O 95.1 REMARK 620 3 ASP B 162 O 68.2 106.9 REMARK 620 4 ASN B 194 O 83.9 76.0 152.0 REMARK 620 5 GLY B 196 O 73.9 162.2 82.4 88.7 REMARK 620 6 ASP B 198 OD1 162.8 102.1 107.0 99.4 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 284 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 128 OD2 REMARK 620 2 ASP B 128 OD1 45.3 REMARK 620 3 ASP B 203 O 146.6 167.1 REMARK 620 4 ASP B 203 OD2 96.5 108.5 78.3 REMARK 620 5 GLU B 205 O 70.0 109.4 78.9 103.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 281 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 116.7 REMARK 620 3 HIS B 187 NE2 118.5 113.3 REMARK 620 4 HIS B 200 ND1 101.1 97.8 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 282 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 87.9 REMARK 620 3 SER B 182 O 83.6 87.5 REMARK 620 4 LEU B 184 O 106.6 165.0 97.8 REMARK 620 5 ASP B 202 OD2 113.8 79.9 157.9 90.4 REMARK 620 6 GLU B 205 OE2 160.7 79.9 81.0 87.0 78.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 280 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 94.8 REMARK 620 3 HIS B 232 NE2 107.8 90.9 REMARK 620 4 FA4 B1002 O33 158.0 96.3 90.9 REMARK 620 5 FA4 B1002 O32 90.9 97.1 159.0 69.0 REMARK 620 6 FA4 B1002 N22 107.4 120.0 130.1 50.7 30.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 271 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 272 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 283 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 284 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 285 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 286 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FA4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FA4 B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D1O RELATED DB: PDB REMARK 900 STROMELYSIN-1 (MMP-3) COMPLEXED TO A HYDROXAMIC ACID INHIBITOR DBREF 2D1N A 104 269 UNP P45452 MMP13_HUMAN 104 269 DBREF 2D1N B 104 269 UNP P45452 MMP13_HUMAN 104 269 SEQRES 1 A 166 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 166 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 166 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 166 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 166 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 166 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 166 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 166 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 166 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 166 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 166 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 166 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 166 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY SEQRES 1 B 166 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 B 166 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 B 166 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 B 166 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 B 166 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 B 166 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 166 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 B 166 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 B 166 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 B 166 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 B 166 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 B 166 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 B 166 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY HET ZN A 270 1 HET ZN A 271 1 HET CA A 272 1 HET CA A 273 1 HET CA A 274 1 HET ZN A 285 1 HET ZN A 286 1 HET FA4 A1001 33 HET ZN B 280 1 HET ZN B 281 1 HET CA B 282 1 HET CA B 283 1 HET CA B 284 1 HET FA4 B1002 33 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM FA4 SM-25453 HETSYN FA4 (2-(9-((R)-1-(HYDROXYCARBAMOYL)-5- HETSYN 2 FA4 AMINOPENTYLCARBAMOYL)NONYL)BENZYL)GUANIDINE; HETSYN 3 FA4 GUANIDINOMETHYLBENZIL D-LYSINE HYDROXAMATE FORMUL 3 ZN 6(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 10 FA4 2(C24 H42 N6 O3) FORMUL 17 HOH *49(H2 O) HELIX 1 1 PHE A 107 LEU A 111 5 5 HELIX 2 2 THR A 130 ASP A 147 1 18 HELIX 3 3 LEU A 216 LEU A 228 1 13 HELIX 4 4 PRO A 255 GLY A 267 1 13 HELIX 5 5 PHE B 107 LEU B 111 5 5 HELIX 6 6 THR B 130 ASP B 147 1 18 HELIX 7 7 LEU B 216 GLY B 229 1 14 HELIX 8 8 PRO B 255 GLY B 267 1 13 SHEET 1 A 5 ASN A 152 ARG A 155 0 SHEET 2 A 5 ASN A 117 ILE A 122 1 N LEU A 118 O ASN A 152 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 O HOH A 7 ZN ZN A 285 1555 1555 2.76 LINK O HOH A 8 ZN ZN A 286 1555 1555 2.68 LINK O HOH A 11 CA CA A 273 1555 1555 2.87 LINK O HOH A 41 CA CA A 273 1555 1555 2.54 LINK OD2 ASP A 128 CA CA A 274 1555 1555 2.43 LINK OD1 ASP A 128 CA CA A 274 1555 1555 3.31 LINK OE1 GLU A 135 ZN ZN A 285 1555 1555 1.92 LINK NE2 HIS A 157 ZN ZN A 286 1555 1555 2.11 LINK O ASP A 162 CA CA A 273 1555 1555 2.44 LINK NE2 HIS A 172 ZN ZN A 271 1555 1555 1.98 LINK OD2 ASP A 174 ZN ZN A 271 1555 1555 1.97 LINK OD1 ASP A 179 CA CA A 272 1555 1555 2.62 LINK O GLY A 180 CA CA A 272 1555 1555 2.30 LINK O SER A 182 CA CA A 272 1555 1555 2.25 LINK O LEU A 184 CA CA A 272 1555 1555 2.29 LINK NE2 HIS A 187 ZN ZN A 271 1555 1555 2.13 LINK O ASN A 194 CA CA A 273 1555 1555 2.40 LINK O GLY A 196 CA CA A 273 1555 1555 2.30 LINK OD1 ASP A 198 CA CA A 273 1555 1555 2.57 LINK ND1 HIS A 200 ZN ZN A 271 1555 1555 1.94 LINK OD2 ASP A 202 CA CA A 272 1555 1555 2.41 LINK OD2 ASP A 203 CA CA A 274 1555 1555 2.52 LINK O ASP A 203 CA CA A 274 1555 1555 2.51 LINK OE2 GLU A 205 CA CA A 272 1555 1555 2.24 LINK O GLU A 205 CA CA A 274 1555 1555 2.30 LINK NE2 HIS A 222 ZN ZN A 270 1555 1555 2.34 LINK NE2 HIS A 226 ZN ZN A 270 1555 1555 2.21 LINK NE2 HIS A 232 ZN ZN A 270 1555 1555 2.04 LINK ZN ZN A 270 O32 FA4 A1001 1555 1555 1.94 LINK ZN ZN A 270 O33 FA4 A1001 1555 1555 2.34 LINK ZN ZN A 285 NE2 HIS B 157 1555 1555 2.18 LINK ZN ZN A 286 OE1 GLU B 135 1555 1555 1.92 LINK O HOH B 18 CA CA B 283 1555 1555 3.09 LINK O HOH B 19 CA CA B 283 1555 1555 2.54 LINK OD2 ASP B 128 CA CA B 284 1555 1555 2.42 LINK OD1 ASP B 128 CA CA B 284 1555 1555 3.08 LINK O ASP B 162 CA CA B 283 1555 1555 2.40 LINK NE2 HIS B 172 ZN ZN B 281 1555 1555 1.96 LINK OD2 ASP B 174 ZN ZN B 281 1555 1555 2.05 LINK OD1 ASP B 179 CA CA B 282 1555 1555 2.42 LINK O GLY B 180 CA CA B 282 1555 1555 2.37 LINK O SER B 182 CA CA B 282 1555 1555 2.23 LINK O LEU B 184 CA CA B 282 1555 1555 2.41 LINK NE2 HIS B 187 ZN ZN B 281 1555 1555 2.02 LINK O ASN B 194 CA CA B 283 1555 1555 2.38 LINK O GLY B 196 CA CA B 283 1555 1555 2.37 LINK OD1 ASP B 198 CA CA B 283 1555 1555 2.37 LINK ND1 HIS B 200 ZN ZN B 281 1555 1555 2.03 LINK OD2 ASP B 202 CA CA B 282 1555 1555 2.47 LINK O ASP B 203 CA CA B 284 1555 1555 2.33 LINK OD2 ASP B 203 CA CA B 284 1555 1555 2.69 LINK OE2 GLU B 205 CA CA B 282 1555 1555 2.40 LINK O GLU B 205 CA CA B 284 1555 1555 2.60 LINK NE2 HIS B 222 ZN ZN B 280 1555 1555 2.24 LINK NE2 HIS B 226 ZN ZN B 280 1555 1555 2.26 LINK NE2 HIS B 232 ZN ZN B 280 1555 1555 2.00 LINK ZN ZN B 280 O33 FA4 B1002 1555 1555 2.53 LINK ZN ZN B 280 O32 FA4 B1002 1555 1555 2.03 LINK ZN ZN B 280 N22 FA4 B1002 1555 1555 2.70 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 FA4 A1001 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 6 HOH A 11 HOH A 41 ASP A 162 ASN A 194 SITE 2 AC4 6 GLY A 196 ASP A 198 SITE 1 AC5 3 ASP A 128 ASP A 203 GLU A 205 SITE 1 AC6 4 HIS B 222 HIS B 226 HIS B 232 FA4 B1002 SITE 1 AC7 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC8 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AC8 6 ASP B 202 GLU B 205 SITE 1 AC9 6 HOH B 18 HOH B 19 ASP B 162 ASN B 194 SITE 2 AC9 6 GLY B 196 ASP B 198 SITE 1 BC1 3 ASP B 128 ASP B 203 GLU B 205 SITE 1 BC2 6 HOH A 3 HOH A 4 HOH A 7 GLU A 135 SITE 2 BC2 6 ARG A 155 HIS B 157 SITE 1 BC3 5 HOH A 8 HIS A 157 HOH B 5 GLU B 135 SITE 2 BC3 5 ARG B 155 SITE 1 BC4 17 TYR A 176 LEU A 184 LEU A 185 ALA A 186 SITE 2 BC4 17 HIS A 222 GLU A 223 HIS A 226 HIS A 232 SITE 3 BC4 17 PRO A 236 ALA A 238 LEU A 239 PHE A 241 SITE 4 BC4 17 PRO A 242 ILE A 243 TYR A 244 THR A 245 SITE 5 BC4 17 ZN A 270 SITE 1 BC5 17 TYR B 176 LEU B 184 LEU B 185 ALA B 186 SITE 2 BC5 17 HIS B 222 GLU B 223 HIS B 226 HIS B 232 SITE 3 BC5 17 PRO B 236 ALA B 238 LEU B 239 PHE B 241 SITE 4 BC5 17 PRO B 242 ILE B 243 TYR B 244 THR B 245 SITE 5 BC5 17 ZN B 280 CRYST1 96.470 96.470 67.520 90.00 90.00 120.00 P 32 6 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 0.010366 0.005985 0.000000 0.00000 SCALE2 0.000000 0.011970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014810 0.00000