HEADER HYDROLASE/HYDROLASE INHIBITOR 12-MAY-14 3WV1 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH 4- TITLE 2 (2-((6-FLUORO-2-((3-METHOXYBENZYL)CARBAMOYL)-4-OXO-3,4- TITLE 3 DIHYDROQUINAZOLIN-5-YL)OXY)ETHYL)BENZOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MMP-13, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.OKI,Y.TANAKA REVDAT 1 20-MAY-15 3WV1 0 JRNL AUTH H.NARA,K.SATO,T.NAITO,H.MOTOTANI,H.OKI,Y.YAMAMOTO,H.KUNO, JRNL AUTH 2 T.SANTOU,N.KANZAKI,J.TERAUCHI,O.UCHIKAWA,M.KORI JRNL TITL DISCOVERY OF NOVEL, HIGHLY POTENT, AND SELECTIVE JRNL TITL 2 QUINAZOLINE-2-CARBOXAMIDE-BASED MATRIX METALLOPROTEINASE JRNL TITL 3 (MMP)-13 INHIBITORS WITHOUT A ZINC BINDING GROUP USING A JRNL TITL 4 STRUCTURE-BASED DESIGN APPROACH JRNL REF J.MED.CHEM. V. 57 8886 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 25264600 JRNL DOI 10.1021/JM500981K REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 24131 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 + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1220 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1256 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2656 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.84000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : -0.72000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.137 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2833 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3849 ; 1.318 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 6.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;37.290 ;24.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 405 ;14.657 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;22.093 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2357 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1387 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1929 ; 0.315 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 228 ; 0.151 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 31 ; 0.131 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 70 ; 0.203 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.130 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1663 ; 1.557 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2669 ; 2.575 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1262 ; 3.746 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1180 ; 5.272 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 104 A 273 REMARK 3 RESIDUE RANGE : A 301 A 307 REMARK 3 ORIGIN FOR THE GROUP (A): 41.4240 -14.1700 -15.7230 REMARK 3 T TENSOR REMARK 3 T11: -0.0039 T22: -0.0444 REMARK 3 T33: -0.0245 T12: -0.0045 REMARK 3 T13: 0.0032 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.7990 L22: 0.3872 REMARK 3 L33: 1.6105 L12: -0.2057 REMARK 3 L13: -0.8716 L23: -0.0096 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: 0.0382 S13: -0.0072 REMARK 3 S21: 0.0694 S22: -0.0417 S23: 0.0043 REMARK 3 S31: -0.0124 S32: 0.0212 S33: 0.0347 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 104 B 269 REMARK 3 RESIDUE RANGE : B 301 B 307 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6740 -22.4690 -26.1330 REMARK 3 T TENSOR REMARK 3 T11: 0.0205 T22: 0.0228 REMARK 3 T33: -0.0467 T12: -0.0770 REMARK 3 T13: 0.0380 T23: 0.0288 REMARK 3 L TENSOR REMARK 3 L11: 0.2014 L22: 0.6702 REMARK 3 L33: 0.7355 L12: -0.0627 REMARK 3 L13: 0.2152 L23: 0.5065 REMARK 3 S TENSOR REMARK 3 S11: 0.0659 S12: -0.0164 S13: -0.0305 REMARK 3 S21: 0.1854 S22: -0.1477 S23: 0.0589 REMARK 3 S31: 0.1276 S32: -0.0362 S33: 0.0818 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-14. REMARK 100 THE RCSB ID CODE IS RCSB096827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32B2 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24131 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 29.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.690 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.21 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-16%(W/V) PEG8000, 1.0-1.5M AMMONIUM REMARK 280 FORMATE, 0.1M TRIS HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 67.18600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.02900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.18600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.02900 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, 3 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 ASN A 274 REMARK 465 PRO B 108 REMARK 465 ARG B 109 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 PRO A 108 152.03 -46.70 REMARK 500 LEU A 111 107.51 -58.06 REMARK 500 LYS A 170 -131.53 44.18 REMARK 500 SER A 182 -169.41 62.16 REMARK 500 ASN A 194 -121.05 60.70 REMARK 500 ASP A 272 -134.76 -101.92 REMARK 500 LYS B 170 -133.53 45.93 REMARK 500 TYR B 176 74.43 -114.58 REMARK 500 SER B 182 -172.16 57.30 REMARK 500 ASN B 194 -122.89 63.76 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 666 DISTANCE = 5.11 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 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 174 OD2 REMARK 620 2 HIS B 172 NE2 109.0 REMARK 620 3 HIS B 187 NE2 113.9 115.1 REMARK 620 4 HIS B 200 ND1 92.8 107.8 115.8 REMARK 620 N 1 2 3 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 ASP A 174 OD2 REMARK 620 2 HIS A 172 NE2 110.8 REMARK 620 3 HIS A 187 NE2 111.1 118.4 REMARK 620 4 HIS A 200 ND1 93.5 112.3 107.9 REMARK 620 N 1 2 3 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 232 NE2 REMARK 620 2 FMT A 306 O2 88.7 REMARK 620 3 HIS A 226 NE2 100.3 124.8 REMARK 620 4 HIS A 222 NE2 112.4 123.7 102.9 REMARK 620 5 FMT A 306 O1 143.7 56.3 93.3 96.9 REMARK 620 N 1 2 3 4 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 226 NE2 REMARK 620 2 HIS B 222 NE2 106.4 REMARK 620 3 HIS B 232 NE2 112.2 103.4 REMARK 620 4 FMT B 306 O2 156.3 93.0 75.0 REMARK 620 5 FMT B 306 O1 104.5 109.4 120.3 55.2 REMARK 620 N 1 2 3 4 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 GLU A 205 OE2 REMARK 620 2 ASP A 202 OD2 91.6 REMARK 620 3 GLY A 180 O 94.9 87.6 REMARK 620 4 LEU A 184 O 82.8 94.7 176.8 REMARK 620 5 ASP A 179 OD1 173.2 95.1 86.1 95.8 REMARK 620 6 SER A 182 O 82.4 170.8 86.0 91.5 91.0 REMARK 620 N 1 2 3 4 5 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 GLU B 205 OE2 REMARK 620 2 LEU B 184 O 86.1 REMARK 620 3 GLY B 180 O 84.7 170.5 REMARK 620 4 ASP B 202 OD2 97.9 97.1 86.4 REMARK 620 5 ASP B 179 OD1 169.8 92.0 96.7 92.3 REMARK 620 6 SER B 182 O 91.4 91.6 86.4 167.8 78.7 REMARK 620 N 1 2 3 4 5 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 GLY B 196 O REMARK 620 2 ASP B 162 O 87.1 REMARK 620 3 ASN B 194 O 99.8 171.8 REMARK 620 4 ASP B 198 OD1 94.5 85.5 89.5 REMARK 620 5 HOH B 611 O 166.0 100.8 73.4 97.6 REMARK 620 6 HOH B 604 O 76.4 93.9 92.1 170.9 91.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 205 O REMARK 620 2 ASP B 128 OD2 81.1 REMARK 620 3 ASP B 203 O 95.9 160.0 REMARK 620 4 ASP B 203 OD1 113.1 98.7 64.0 REMARK 620 5 HOH B 657 O 73.3 92.6 105.6 167.7 REMARK 620 N 1 2 3 4 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 162 O REMARK 620 2 GLY A 196 O 90.3 REMARK 620 3 ASP A 198 OD1 89.9 88.3 REMARK 620 4 ASN A 194 O 173.5 96.0 92.1 REMARK 620 5 HOH A 605 O 90.7 173.8 97.8 82.9 REMARK 620 6 HOH A 698 O 90.7 81.6 169.9 88.4 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 GLU A 205 O 81.0 REMARK 620 3 ASP A 203 O 156.2 91.5 REMARK 620 4 ASP A 203 OD1 90.9 106.4 69.4 REMARK 620 5 HOH A 696 O 127.8 98.3 75.6 137.1 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 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 NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WHH A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WHH B 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WV2 RELATED DB: PDB REMARK 900 RELATED ID: 3WV3 RELATED DB: PDB DBREF 3WV1 A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 3WV1 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 NA A 305 1 HET FMT A 306 3 HET WHH A 307 36 HET ZN B 301 1 HET ZN B 302 1 HET CA B 303 1 HET CA B 304 1 HET NA B 305 1 HET FMT B 306 3 HET WHH B 307 36 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM FMT FORMIC ACID HETNAM WHH 4-[2-({6-FLUORO-2-[(3-METHOXYBENZYL)CARBAMOYL]-4-OXO-3, HETNAM 2 WHH 4-DIHYDROQUINAZOLIN-5-YL}OXY)ETHYL]BENZOIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 4(CA 2+) FORMUL 7 NA 2(NA 1+) FORMUL 8 FMT 2(C H2 O2) FORMUL 9 WHH 2(C26 H22 F N3 O6) FORMUL 17 HOH *246(H2 O) HELIX 1 1 THR A 130 ASP A 147 1 18 HELIX 2 2 LEU A 216 LEU A 228 1 13 HELIX 3 3 PRO A 255 GLY A 267 1 13 HELIX 4 4 THR B 130 ASP B 147 1 18 HELIX 5 5 LEU B 216 LEU B 228 1 13 HELIX 6 6 PRO B 255 GLY B 267 1 13 SHEET 1 A 5 ASN A 152 LEU A 156 0 SHEET 2 A 5 ASN A 117 ILE A 122 1 N TYR A 120 O LEU A 156 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 ALA B 199 N MET B 164 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 OD2 ASP B 174 ZN ZN B 302 1555 1555 1.82 LINK OD2 ASP A 174 ZN ZN A 302 1555 1555 1.93 LINK NE2 HIS B 172 ZN ZN B 302 1555 1555 1.94 LINK NE2 HIS A 172 ZN ZN A 302 1555 1555 1.96 LINK NE2 HIS B 187 ZN ZN B 302 1555 1555 1.97 LINK NE2 HIS A 187 ZN ZN A 302 1555 1555 2.01 LINK ND1 HIS B 200 ZN ZN B 302 1555 1555 2.05 LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.05 LINK ZN ZN A 301 O2 FMT A 306 1555 1555 2.07 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.10 LINK ND1 HIS A 200 ZN ZN A 302 1555 1555 2.10 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.12 LINK OE2 GLU A 205 CA CA A 303 1555 1555 2.13 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.13 LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 2.15 LINK NE2 HIS B 232 ZN ZN B 301 1555 1555 2.18 LINK OD2 ASP A 202 CA CA A 303 1555 1555 2.22 LINK ZN ZN B 301 O2 FMT B 306 1555 1555 2.23 LINK OE2 GLU B 205 CA CA B 303 1555 1555 2.23 LINK O GLY A 180 CA CA A 303 1555 1555 2.24 LINK O LEU B 184 CA CA B 303 1555 1555 2.24 LINK O GLY B 196 CA CA B 304 1555 1555 2.25 LINK O LEU A 184 CA CA A 303 1555 1555 2.27 LINK O GLU B 205 NA NA B 305 1555 1555 2.27 LINK O ASP B 162 CA CA B 304 1555 1555 2.27 LINK O ASP A 162 CA CA A 304 1555 1555 2.29 LINK O GLY A 196 CA CA A 304 1555 1555 2.29 LINK O GLY B 180 CA CA B 303 1555 1555 2.29 LINK OD1 ASP A 179 CA CA A 303 1555 1555 2.30 LINK OD2 ASP B 202 CA CA B 303 1555 1555 2.32 LINK OD1 ASP B 179 CA CA B 303 1555 1555 2.33 LINK O SER A 182 CA CA A 303 1555 1555 2.33 LINK O ASN B 194 CA CA B 304 1555 1555 2.35 LINK OD1 ASP A 198 CA CA A 304 1555 1555 2.38 LINK O ASN A 194 CA CA A 304 1555 1555 2.40 LINK ZN ZN A 301 O1 FMT A 306 1555 1555 2.41 LINK OD2 ASP A 128 NA NA A 305 1555 1555 2.41 LINK O GLU A 205 NA NA A 305 1555 1555 2.41 LINK O SER B 182 CA CA B 303 1555 1555 2.45 LINK OD2 ASP B 128 NA NA B 305 1555 1555 2.46 LINK ZN ZN B 301 O1 FMT B 306 1555 1555 2.46 LINK OD1 ASP B 198 CA CA B 304 1555 1555 2.52 LINK O ASP B 203 NA NA B 305 1555 1555 2.70 LINK O ASP A 203 NA NA A 305 1555 1555 2.81 LINK OD1 ASP A 203 NA NA A 305 1555 1555 2.86 LINK OD1 ASP B 203 NA NA B 305 1555 1555 2.98 LINK CA CA B 304 O HOH B 611 1555 1555 2.29 LINK CA CA A 304 O HOH A 605 1555 1555 2.32 LINK CA CA A 304 O HOH A 698 1555 1555 2.36 LINK CA CA B 304 O HOH B 604 1555 1555 2.43 LINK NA NA B 305 O HOH B 657 1555 1555 2.69 LINK NA NA A 305 O HOH A 696 1555 1555 3.16 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 FMT A 306 SITE 1 AC2 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC3 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC3 6 ASP A 202 GLU A 205 SITE 1 AC4 6 ASP A 162 ASN A 194 GLY A 196 ASP A 198 SITE 2 AC4 6 HOH A 605 HOH A 698 SITE 1 AC5 3 ASP A 128 ASP A 203 GLU A 205 SITE 1 AC6 7 ALA A 186 HIS A 222 GLU A 223 HIS A 226 SITE 2 AC6 7 HIS A 232 ZN A 301 HOH A 715 SITE 1 AC7 19 LYS A 140 ASN A 215 PHE A 217 LEU A 218 SITE 2 AC7 19 HIS A 222 ALA A 238 LEU A 239 PHE A 241 SITE 3 AC7 19 ILE A 243 TYR A 244 THR A 245 TYR A 246 SITE 4 AC7 19 THR A 247 LYS A 249 PHE A 252 MET A 253 SITE 5 AC7 19 PRO A 255 HOH A 647 HOH A 743 SITE 1 AC8 4 HIS B 222 HIS B 226 HIS B 232 FMT B 306 SITE 1 AC9 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 BC1 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 BC1 6 ASP B 202 GLU B 205 SITE 1 BC2 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 BC2 6 HOH B 604 HOH B 611 SITE 1 BC3 4 ASP B 128 ASP B 203 GLU B 205 HOH B 657 SITE 1 BC4 5 HIS B 222 GLU B 223 HIS B 226 HIS B 232 SITE 2 BC4 5 ZN B 301 SITE 1 BC5 19 LYS B 140 ASN B 215 PHE B 217 LEU B 218 SITE 2 BC5 19 HIS B 222 GLU B 223 ALA B 238 LEU B 239 SITE 3 BC5 19 PHE B 241 ILE B 243 TYR B 244 THR B 245 SITE 4 BC5 19 THR B 247 LYS B 249 PHE B 252 MET B 253 SITE 5 BC5 19 PRO B 255 HOH B 672 HOH B 682 CRYST1 134.372 36.058 95.298 90.00 130.90 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 0.007442 0.000000 0.006445 0.00000 SCALE2 0.000000 0.027733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013882 0.00000 MASTER 511 0 14 6 14 0 28 6 0 0 0 28 END