HEADER HYDROLASE/HYDROLASE INHIBITOR 12-MAY-14 3WV2 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH N- TITLE 2 (3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROQUINAZOLINE-2-CARBOXAMIDE 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 HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.OKI,Y.TANAKA REVDAT 2 24-AUG-22 3WV2 1 JRNL REMARK LINK REVDAT 1 24-SEP-14 3WV2 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 THIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDES BEARING A JRNL TITL 2 CARBOXYBENZENE GROUP AT 5-POSITION: HIGHLY POTENT, JRNL TITL 3 SELECTIVE, AND ORALLY AVAILABLE MMP-13 INHIBITORS JRNL TITL 4 INTERACTING WITH THE S1′′ BINDING SITE. JRNL REF BIOORG.MED.CHEM. V. 22 5487 2014 JRNL REFN ESSN 1464-3391 JRNL PMID 25192810 JRNL DOI 10.1016/J.BMC.2014.07.025 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 14007 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 734 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1056 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2611 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -1.67000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.56000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.461 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.694 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2753 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3741 ; 1.223 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 322 ; 6.181 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;36.301 ;24.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 395 ;16.097 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;23.042 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2257 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 272 REMARK 3 RESIDUE RANGE : A 301 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2200 -21.7480 41.8260 REMARK 3 T TENSOR REMARK 3 T11: 0.0173 T22: 0.0303 REMARK 3 T33: 0.0716 T12: 0.0020 REMARK 3 T13: -0.0054 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.4329 L22: 0.4915 REMARK 3 L33: 0.9188 L12: -0.1841 REMARK 3 L13: -0.8314 L23: 0.2039 REMARK 3 S TENSOR REMARK 3 S11: 0.0340 S12: -0.0289 S13: -0.0070 REMARK 3 S21: -0.0632 S22: -0.0383 S23: -0.0477 REMARK 3 S31: -0.0231 S32: -0.0078 S33: 0.0043 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 268 REMARK 3 RESIDUE RANGE : B 301 B 305 REMARK 3 ORIGIN FOR THE GROUP (A): -25.2590 -13.9720 12.6170 REMARK 3 T TENSOR REMARK 3 T11: 0.0340 T22: 0.1356 REMARK 3 T33: 0.1388 T12: -0.0406 REMARK 3 T13: 0.0040 T23: 0.0928 REMARK 3 L TENSOR REMARK 3 L11: 0.1732 L22: 0.9913 REMARK 3 L33: 0.6557 L12: -0.3697 REMARK 3 L13: 0.1567 L23: -0.0901 REMARK 3 S TENSOR REMARK 3 S11: 0.0218 S12: 0.0519 S13: 0.0795 REMARK 3 S21: -0.0328 S22: -0.1719 S23: -0.1642 REMARK 3 S31: -0.0480 S32: 0.1121 S33: 0.1501 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 3WV2 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 DEPOSITION ID IS D_1000096828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-03 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 : D*TREK 7.1SSI, CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14744 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 4.030 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.98 REMARK 200 R MERGE FOR SHELL (I) : 0.20100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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 (%): 44.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5UM ZN(OAC)2, 5MM CACL2, 50MM NACL, REMARK 280 20MM 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 71.76500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.85950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.76500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.85950 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: 2250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 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 GLY A 248 REMARK 465 LYS A 249 REMARK 465 SER A 250 REMARK 465 PRO A 273 REMARK 465 ASN A 274 REMARK 465 PRO B 108 REMARK 465 ARG B 109 REMARK 465 LYS B 249 REMARK 465 SER B 250 REMARK 465 GLY B 269 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 REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE1 HIS B 251 O HOH A 608 3454 2.16 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 LYS A 170 -135.48 53.47 REMARK 500 SER A 182 -170.89 61.41 REMARK 500 ASN A 194 -113.02 61.72 REMARK 500 SER A 210 -159.60 -134.41 REMARK 500 LYS B 170 -132.08 47.09 REMARK 500 ASP B 174 12.06 -142.29 REMARK 500 PHE B 175 17.94 55.80 REMARK 500 TYR B 176 77.27 -111.62 REMARK 500 SER B 182 -164.93 56.70 REMARK 500 ASN B 194 -123.55 65.62 REMARK 500 SER B 210 -158.02 -141.39 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 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 203 OD1 92.2 REMARK 620 3 ASP A 203 O 164.3 73.8 REMARK 620 4 GLU A 205 O 81.7 108.8 96.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 171.1 REMARK 620 3 GLY A 196 O 90.2 97.9 REMARK 620 4 ASP A 198 OD1 87.2 96.3 92.1 REMARK 620 5 HOH A 693 O 92.6 78.8 170.8 96.7 REMARK 620 6 HOH A 695 O 89.6 88.2 79.0 170.6 92.3 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 172 NE2 REMARK 620 2 ASP A 174 OD2 107.7 REMARK 620 3 HIS A 187 NE2 119.2 117.9 REMARK 620 4 HIS A 200 ND1 110.9 89.5 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 85.0 REMARK 620 3 SER A 182 O 85.0 83.6 REMARK 620 4 LEU A 184 O 93.7 178.1 94.9 REMARK 620 5 ASP A 202 OD2 92.5 91.0 174.2 90.5 REMARK 620 6 GLU A 205 OE2 169.3 90.4 84.9 90.7 97.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 96.9 REMARK 620 3 HIS A 232 NE2 111.6 100.9 REMARK 620 4 HOH A 602 O 108.1 109.8 125.5 REMARK 620 N 1 2 3 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 ASP B 128 OD2 REMARK 620 2 ASP B 128 OD1 47.3 REMARK 620 3 ASP B 203 O 152.3 160.2 REMARK 620 4 ASP B 203 OD1 95.3 105.1 75.4 REMARK 620 5 GLU B 205 O 75.8 115.9 82.0 107.1 REMARK 620 6 HOH B 476 O 118.1 70.8 89.5 100.2 148.2 REMARK 620 7 HOH B 486 O 90.6 78.6 99.6 174.1 74.8 76.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 176.1 REMARK 620 3 GLY B 196 O 82.9 95.7 REMARK 620 4 ASP B 198 OD1 89.4 94.3 93.4 REMARK 620 5 HOH B 470 O 101.7 78.3 157.9 108.2 REMARK 620 6 HOH B 489 O 81.5 94.7 78.4 168.4 80.9 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 172 NE2 REMARK 620 2 ASP B 174 OD2 113.7 REMARK 620 3 HIS B 187 NE2 115.0 111.2 REMARK 620 4 HIS B 200 ND1 112.9 89.4 112.0 REMARK 620 N 1 2 3 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 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 96.5 REMARK 620 3 SER B 182 O 82.8 88.1 REMARK 620 4 LEU B 184 O 87.6 175.7 91.4 REMARK 620 5 ASP B 202 OD2 89.6 85.5 169.4 95.7 REMARK 620 6 GLU B 205 OE2 167.1 92.2 88.0 83.6 100.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 105.4 REMARK 620 3 HIS B 232 NE2 101.4 110.2 REMARK 620 4 HOH B 473 O 110.5 111.3 117.0 REMARK 620 N 1 2 3 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 WGG A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WGG B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WV1 RELATED DB: PDB REMARK 900 RELATED ID: 3WV3 RELATED DB: PDB DBREF 3WV2 A 104 274 UNP P45452 MMP13_HUMAN 104 274 DBREF 3WV2 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 WGG A 306 23 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 WGG B 306 23 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM WGG N-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROQUINAZOLINE-2- HETNAM 2 WGG CARBOXAMIDE FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 4(CA 2+) FORMUL 7 NA 2(NA 1+) FORMUL 8 WGG 2(C17 H15 N3 O3) FORMUL 15 HOH *266(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 LEU B 156 0 SHEET 2 C 5 ASN B 117 ILE B 122 1 N TYR B 120 O LEU B 156 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 OD2 ASP A 128 NA NA A 305 1555 1555 2.23 LINK O ASP A 162 CA CA A 304 1555 1555 2.36 LINK NE2 HIS A 172 ZN ZN A 302 1555 1555 1.95 LINK OD2 ASP A 174 ZN ZN A 302 1555 1555 1.86 LINK OD1 ASP A 179 CA CA A 303 1555 1555 2.32 LINK O GLY A 180 CA CA A 303 1555 1555 2.24 LINK O SER A 182 CA CA A 303 1555 1555 2.35 LINK O LEU A 184 CA CA A 303 1555 1555 2.30 LINK NE2 HIS A 187 ZN ZN A 302 1555 1555 2.02 LINK O ASN A 194 CA CA A 304 1555 1555 2.32 LINK O GLY A 196 CA CA A 304 1555 1555 2.30 LINK OD1 ASP A 198 CA CA A 304 1555 1555 2.36 LINK ND1 HIS A 200 ZN ZN A 302 1555 1555 2.06 LINK OD2 ASP A 202 CA CA A 303 1555 1555 2.29 LINK OD1 ASP A 203 NA NA A 305 1555 1555 2.54 LINK O ASP A 203 NA NA A 305 1555 1555 2.67 LINK OE2 GLU A 205 CA CA A 303 1555 1555 2.25 LINK O GLU A 205 NA NA A 305 1555 1555 2.40 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.09 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.03 LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.03 LINK ZN ZN A 301 O HOH A 602 1555 1555 2.43 LINK CA CA A 304 O HOH A 693 1555 1555 2.37 LINK CA CA A 304 O HOH A 695 1555 1555 2.47 LINK OD2 ASP B 128 NA NA B 305 1555 1555 2.40 LINK OD1 ASP B 128 NA NA B 305 1555 1555 2.93 LINK O ASP B 162 CA CA B 304 1555 1555 2.24 LINK NE2 HIS B 172 ZN ZN B 302 1555 1555 1.96 LINK OD2 ASP B 174 ZN ZN B 302 1555 1555 1.94 LINK OD1 ASP B 179 CA CA B 303 1555 1555 2.50 LINK O GLY B 180 CA CA B 303 1555 1555 2.33 LINK O SER B 182 CA CA B 303 1555 1555 2.31 LINK O LEU B 184 CA CA B 303 1555 1555 2.22 LINK NE2 HIS B 187 ZN ZN B 302 1555 1555 2.06 LINK O ASN B 194 CA CA B 304 1555 1555 2.26 LINK O GLY B 196 CA CA B 304 1555 1555 2.32 LINK OD1 ASP B 198 CA CA B 304 1555 1555 2.39 LINK ND1 HIS B 200 ZN ZN B 302 1555 1555 2.09 LINK OD2 ASP B 202 CA CA B 303 1555 1555 2.29 LINK O ASP B 203 NA NA B 305 1555 1555 2.34 LINK OD1 ASP B 203 NA NA B 305 1555 1555 2.57 LINK OE2 GLU B 205 CA CA B 303 1555 1555 2.25 LINK O GLU B 205 NA NA B 305 1555 1555 2.41 LINK NE2 HIS B 222 ZN ZN B 301 1555 1555 2.15 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 1.99 LINK NE2 HIS B 232 ZN ZN B 301 1555 1555 2.08 LINK ZN ZN B 301 O HOH B 473 1555 1555 2.36 LINK CA CA B 304 O HOH B 470 1555 1555 2.39 LINK CA CA B 304 O HOH B 489 1555 1555 2.57 LINK NA NA B 305 O HOH B 476 1555 1555 2.36 LINK NA NA B 305 O HOH B 486 1555 1555 2.59 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 HOH A 602 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 693 HOH A 695 SITE 1 AC5 3 ASP A 128 ASP A 203 GLU A 205 SITE 1 AC6 17 LEU A 218 VAL A 219 HIS A 222 GLU A 223 SITE 2 AC6 17 ALA A 238 LEU A 239 PHE A 241 PRO A 242 SITE 3 AC6 17 ILE A 243 TYR A 244 THR A 245 TYR A 246 SITE 4 AC6 17 THR A 247 PHE A 252 MET A 253 PRO A 255 SITE 5 AC6 17 HOH A 615 SITE 1 AC7 4 HIS B 222 HIS B 226 HIS B 232 HOH B 473 SITE 1 AC8 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC9 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AC9 6 ASP B 202 GLU B 205 SITE 1 BC1 6 ASP B 162 ASN B 194 GLY B 196 ASP B 198 SITE 2 BC1 6 HOH B 470 HOH B 489 SITE 1 BC2 5 ASP B 128 ASP B 203 GLU B 205 HOH B 476 SITE 2 BC2 5 HOH B 486 SITE 1 BC3 13 LEU B 218 HIS B 222 GLU B 223 ALA B 238 SITE 2 BC3 13 LEU B 239 PHE B 241 ILE B 243 TYR B 244 SITE 3 BC3 13 THR B 245 THR B 247 PHE B 252 MET B 253 SITE 4 BC3 13 HOH B 411 CRYST1 143.530 35.719 94.762 90.00 135.29 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 0.006967 0.000000 0.007038 0.00000 SCALE2 0.000000 0.027997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015000 0.00000