HEADER HYDROLASE 30-AUG-05 2D1O TITLE STROMELYSIN-1 (MMP-3) COMPLEXED TO A HYDROXAMIC ACID INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMELYSIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL CATALYTIC DOMAIN; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-3, MMP-3, TRANSIN-1, SL-1; COMPND 6 EC: 3.4.24.17; 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 3 25-OCT-23 2D1O 1 REMARK HETSYN LINK REVDAT 2 24-FEB-09 2D1O 1 VERSN REVDAT 1 27-JUN-06 2D1O 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. 2.02 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 493579.570 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 26663 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) : 0.183 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2651 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3476 REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE : 0.2240 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 369 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.42000 REMARK 3 B22 (A**2) : 1.53000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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 : 0.41 REMARK 3 BSOL : 55.89 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 2D1O 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_1000024877. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 298.0 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 : MACSCIENCE 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 : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26846 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 28.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 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) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.2 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 2SRT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, MPD, HEPES, PH 7.5, VAPOR REMARK 280 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 52.68000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.68000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.47500 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 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 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 ASP B 251 REMARK 465 SER B 252 REMARK 465 PRO B 253 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 ARG A 149 -135.32 47.71 REMARK 500 ASN A 162 -115.11 58.78 REMARK 500 ASP A 189 -155.71 -115.29 REMARK 500 PHE A 210 -164.94 -103.73 REMARK 500 PRO A 221 74.42 -68.84 REMARK 500 ARG B 149 -136.78 51.90 REMARK 500 HIS B 151 21.54 -140.24 REMARK 500 ASN B 162 -121.47 56.11 REMARK 500 ASP B 189 -154.95 -123.72 REMARK 500 PRO B 221 71.04 -66.82 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 260 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 OD2 REMARK 620 2 ASP A 107 OD1 52.8 REMARK 620 3 ASP A 182 OD2 93.8 99.5 REMARK 620 4 ASP A 182 O 151.4 153.9 75.1 REMARK 620 5 GLU A 184 O 77.8 123.3 110.8 81.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 261 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 141 O REMARK 620 2 GLY A 173 O 168.5 REMARK 620 3 ASN A 175 O 103.0 86.2 REMARK 620 4 ASP A 177 OD2 89.3 96.8 95.5 REMARK 620 5 HOH A1022 O 91.6 77.6 156.8 102.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 258 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 151 NE2 REMARK 620 2 ASP A 153 OD2 106.6 REMARK 620 3 HIS A 166 NE2 125.5 110.5 REMARK 620 4 HIS A 179 ND1 106.4 96.3 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 259 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 158 OD2 REMARK 620 2 GLY A 159 O 89.5 REMARK 620 3 GLY A 161 O 85.7 90.4 REMARK 620 4 VAL A 163 O 94.3 176.3 90.1 REMARK 620 5 ASP A 181 OD2 91.7 83.4 173.4 96.2 REMARK 620 6 GLU A 184 OE2 168.5 80.2 89.2 96.1 92.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 257 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 201 NE2 REMARK 620 2 HIS A 205 NE2 97.1 REMARK 620 3 HIS A 211 NE2 102.8 97.1 REMARK 620 4 FA4 A1001 O32 111.3 89.5 144.1 REMARK 620 5 FA4 A1001 O33 110.4 152.2 80.9 77.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 265 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 107 OD2 REMARK 620 2 ASP B 107 OD1 52.5 REMARK 620 3 ASP B 182 OD2 93.8 94.6 REMARK 620 4 ASP B 182 O 151.6 148.7 70.7 REMARK 620 5 GLU B 184 O 78.7 126.2 111.7 85.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 266 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 141 O REMARK 620 2 GLY B 173 O 170.1 REMARK 620 3 ASN B 175 O 104.0 82.0 REMARK 620 4 ASP B 177 OD1 92.1 95.2 95.5 REMARK 620 5 HOH B1005 O 82.5 90.5 83.5 174.0 REMARK 620 6 HOH B1010 O 92.1 80.6 160.0 95.8 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 263 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 151 NE2 REMARK 620 2 ASP B 153 OD2 101.4 REMARK 620 3 HIS B 166 NE2 107.8 123.6 REMARK 620 4 HIS B 179 ND1 110.6 98.9 113.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 264 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 158 OD1 REMARK 620 2 GLY B 159 O 86.9 REMARK 620 3 GLY B 161 O 84.3 88.1 REMARK 620 4 VAL B 163 O 94.5 175.8 88.0 REMARK 620 5 ASP B 181 OD2 96.9 89.5 177.3 94.3 REMARK 620 6 GLU B 184 OE2 170.4 84.3 91.7 94.0 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 262 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 201 NE2 REMARK 620 2 HIS B 205 NE2 94.7 REMARK 620 3 HIS B 211 NE2 106.6 87.9 REMARK 620 4 FA4 B1002 O33 112.1 153.2 82.8 REMARK 620 5 FA4 B1002 O32 101.5 96.9 151.0 80.1 REMARK 620 N 1 2 3 4 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 257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FA4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 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: 2D1N RELATED DB: PDB REMARK 900 COLLAGENASE-3 (MMP-13) COMPLEXED TO A HYDROXAMIC ACID INHIBITOR DBREF 2D1O A 83 253 UNP P08254 MMP3_HUMAN 100 270 DBREF 2D1O B 83 253 UNP P08254 MMP3_HUMAN 100 270 SEQRES 1 A 171 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 A 171 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 A 171 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 A 171 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 A 171 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 A 171 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 171 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 A 171 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 A 171 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 A 171 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 A 171 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 A 171 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 A 171 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 A 171 SER PRO SEQRES 1 B 171 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 B 171 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 B 171 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 B 171 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 B 171 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 B 171 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 171 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 B 171 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 B 171 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 B 171 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 B 171 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 B 171 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 B 171 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 B 171 SER PRO HET ZN A 257 1 HET ZN A 258 1 HET CA A 259 1 HET CA A 260 1 HET CA A 261 1 HET FA4 A1001 33 HET ZN B 262 1 HET ZN B 263 1 HET CA B 264 1 HET CA B 265 1 HET CA B 266 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 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 FA4 2(C24 H42 N6 O3) FORMUL 15 HOH *205(H2 O) HELIX 1 1 PRO A 109 GLU A 126 1 18 HELIX 2 2 LEU A 195 LEU A 207 1 13 HELIX 3 3 ASP A 228 PHE A 232 5 5 HELIX 4 4 SER A 235 GLY A 247 1 13 HELIX 5 5 PRO B 109 GLU B 126 1 18 HELIX 6 6 LEU B 195 GLY B 208 1 14 HELIX 7 7 ASP B 228 PHE B 232 5 5 HELIX 8 8 SER B 235 GLY B 247 1 13 SHEET 1 A 5 THR A 131 ARG A 134 0 SHEET 2 A 5 HIS A 96 ILE A 101 1 N LEU A 97 O THR A 131 SHEET 3 A 5 ILE A 142 ALA A 147 1 O ILE A 144 N ARG A 100 SHEET 4 A 5 ALA A 178 ASP A 181 1 O PHE A 180 N ALA A 147 SHEET 5 A 5 ALA A 165 ALA A 167 -1 N HIS A 166 O HIS A 179 SHEET 1 B 2 TRP A 186 THR A 187 0 SHEET 2 B 2 THR A 193 ASN A 194 1 O THR A 193 N THR A 187 SHEET 1 C 5 THR B 131 ARG B 134 0 SHEET 2 C 5 HIS B 96 ILE B 101 1 N LEU B 97 O THR B 131 SHEET 3 C 5 ILE B 142 ALA B 147 1 O ILE B 144 N ARG B 100 SHEET 4 C 5 ALA B 178 ASP B 181 1 O PHE B 180 N ALA B 147 SHEET 5 C 5 ALA B 165 ALA B 167 -1 N HIS B 166 O HIS B 179 SHEET 1 D 2 TRP B 186 THR B 187 0 SHEET 2 D 2 THR B 193 ASN B 194 1 O THR B 193 N THR B 187 LINK OD2 ASP A 107 CA CA A 260 1555 1555 2.28 LINK OD1 ASP A 107 CA CA A 260 1555 1555 2.62 LINK O ASP A 141 CA CA A 261 1555 1555 2.35 LINK NE2 HIS A 151 ZN ZN A 258 1555 1555 2.04 LINK OD2 ASP A 153 ZN ZN A 258 1555 1555 1.98 LINK OD2 ASP A 158 CA CA A 259 1555 1555 2.44 LINK O GLY A 159 CA CA A 259 1555 1555 2.19 LINK O GLY A 161 CA CA A 259 1555 1555 2.49 LINK O VAL A 163 CA CA A 259 1555 1555 2.20 LINK NE2 HIS A 166 ZN ZN A 258 1555 1555 2.04 LINK O GLY A 173 CA CA A 261 1555 1555 2.40 LINK O ASN A 175 CA CA A 261 1555 1555 2.42 LINK OD2 ASP A 177 CA CA A 261 1555 1555 2.31 LINK ND1 HIS A 179 ZN ZN A 258 1555 1555 2.14 LINK OD2 ASP A 181 CA CA A 259 1555 1555 2.38 LINK OD2 ASP A 182 CA CA A 260 1555 1555 2.32 LINK O ASP A 182 CA CA A 260 1555 1555 2.32 LINK OE2 GLU A 184 CA CA A 259 1555 1555 2.21 LINK O GLU A 184 CA CA A 260 1555 1555 2.44 LINK NE2 HIS A 201 ZN ZN A 257 1555 1555 2.20 LINK NE2 HIS A 205 ZN ZN A 257 1555 1555 2.16 LINK NE2 HIS A 211 ZN ZN A 257 1555 1555 2.14 LINK ZN ZN A 257 O32 FA4 A1001 1555 1555 2.28 LINK ZN ZN A 257 O33 FA4 A1001 1555 1555 2.10 LINK CA CA A 261 O HOH A1022 1555 1555 2.39 LINK OD2 ASP B 107 CA CA B 265 1555 1555 2.26 LINK OD1 ASP B 107 CA CA B 265 1555 1555 2.65 LINK O ASP B 141 CA CA B 266 1555 1555 2.36 LINK NE2 HIS B 151 ZN ZN B 263 1555 1555 2.12 LINK OD2 ASP B 153 ZN ZN B 263 1555 1555 2.01 LINK OD1 ASP B 158 CA CA B 264 1555 1555 2.38 LINK O GLY B 159 CA CA B 264 1555 1555 2.24 LINK O GLY B 161 CA CA B 264 1555 1555 2.37 LINK O VAL B 163 CA CA B 264 1555 1555 2.27 LINK NE2 HIS B 166 ZN ZN B 263 1555 1555 2.13 LINK O GLY B 173 CA CA B 266 1555 1555 2.37 LINK O ASN B 175 CA CA B 266 1555 1555 2.34 LINK OD1 ASP B 177 CA CA B 266 1555 1555 2.35 LINK ND1 HIS B 179 ZN ZN B 263 1555 1555 2.13 LINK OD2 ASP B 181 CA CA B 264 1555 1555 2.36 LINK OD2 ASP B 182 CA CA B 265 1555 1555 2.39 LINK O ASP B 182 CA CA B 265 1555 1555 2.39 LINK OE2 GLU B 184 CA CA B 264 1555 1555 2.23 LINK O GLU B 184 CA CA B 265 1555 1555 2.43 LINK NE2 HIS B 201 ZN ZN B 262 1555 1555 2.18 LINK NE2 HIS B 205 ZN ZN B 262 1555 1555 2.20 LINK NE2 HIS B 211 ZN ZN B 262 1555 1555 2.14 LINK ZN ZN B 262 O33 FA4 B1002 1555 1555 2.03 LINK ZN ZN B 262 O32 FA4 B1002 1555 1555 2.24 LINK CA CA B 266 O HOH B1005 1555 1555 2.43 LINK CA CA B 266 O HOH B1010 1555 1555 2.45 SITE 1 AC1 4 HIS A 201 HIS A 205 HIS A 211 FA4 A1001 SITE 1 AC2 4 HIS A 151 ASP A 153 HIS A 166 HIS A 179 SITE 1 AC3 6 ASP A 158 GLY A 159 GLY A 161 VAL A 163 SITE 2 AC3 6 ASP A 181 GLU A 184 SITE 1 AC4 3 ASP A 107 ASP A 182 GLU A 184 SITE 1 AC5 5 ASP A 141 GLY A 173 ASN A 175 ASP A 177 SITE 2 AC5 5 HOH A1022 SITE 1 AC6 4 HIS B 201 HIS B 205 HIS B 211 FA4 B1002 SITE 1 AC7 4 HIS B 151 ASP B 153 HIS B 166 HIS B 179 SITE 1 AC8 6 ASP B 158 GLY B 159 GLY B 161 VAL B 163 SITE 2 AC8 6 ASP B 181 GLU B 184 SITE 1 AC9 3 ASP B 107 ASP B 182 GLU B 184 SITE 1 BC1 6 ASP B 141 GLY B 173 ASN B 175 ASP B 177 SITE 2 BC1 6 HOH B1005 HOH B1010 SITE 1 BC2 18 ASN A 162 VAL A 163 LEU A 164 ALA A 165 SITE 2 BC2 18 HIS A 201 GLU A 202 HIS A 205 HIS A 211 SITE 3 BC2 18 THR A 215 ALA A 217 LEU A 218 TYR A 220 SITE 4 BC2 18 LEU A 222 TYR A 223 ZN A 257 HOH A1005 SITE 5 BC2 18 HOH A1034 HIS B 224 SITE 1 BC3 19 HIS A 224 ASN B 162 VAL B 163 LEU B 164 SITE 2 BC3 19 ALA B 165 HIS B 201 GLU B 202 HIS B 205 SITE 3 BC3 19 HIS B 211 THR B 215 ALA B 217 LEU B 218 SITE 4 BC3 19 TYR B 220 LEU B 222 TYR B 223 ZN B 262 SITE 5 BC3 19 HOH B1006 HOH B1030 HOH B1046 CRYST1 105.360 50.950 80.790 90.00 105.00 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 0.009491 0.000000 0.002543 0.00000 SCALE2 0.000000 0.019627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012814 0.00000