HEADER HYDROLASE/HYDROLASE INHIBITOR 26-OCT-09 3KEJ TITLE CRYSTAL STRUCTURE OF HUMAN MMP-13 COMPLEXED WITH A (PYRIDIN-4-YL)-2H- TITLE 2 TETRAZOLE COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 104-270; 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)/PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEMEX1 KEYWDS S1' INHIBITOR, SELECTIVE MMP-13 INHIBITOR, S1' SPECIFICITY POCKET, NO KEYWDS 2 CONTACT TO ZN, COLLAGEN DEGRADATION, DISEASE MUTATION, DISULFIDE KEYWDS 3 BOND, EXTRACELLULAR MATRIX, GLYCOPROTEIN, HYDROLASE, METAL-BINDING, KEYWDS 4 METALLOPROTEASE, PROTEASE, SECRETED, ZYMOGEN, HYDROLASE-HYDROLASE KEYWDS 5 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.-S.SHIEH,B.COLLINS,M.E.SCHNUTE REVDAT 2 21-FEB-24 3KEJ 1 REMARK LINK REVDAT 1 10-NOV-10 3KEJ 0 JRNL AUTH M.E.SCHNUTE,P.M.O'BRIEN,J.NAHRA,M.MORRIS,W.HOWARD ROARK, JRNL AUTH 2 C.E.HANAU,P.G.RUMINSKI,J.A.SCHOLTEN,T.R.FLETCHER,B.C.HAMPER, JRNL AUTH 3 J.N.CARROLL,W.C.PATT,H.S.SHIEH,B.COLLINS,A.G.PAVLOVSKY, JRNL AUTH 4 K.E.PALMQUIST,K.W.ASTON,J.HITCHCOCK,M.D.ROGERS,J.MCDONALD, JRNL AUTH 5 A.R.JOHNSON,G.E.MUNIE,A.J.WITTWER,C.F.MAN,S.L.SETTLE, JRNL AUTH 6 O.NEMIROVSKIY,L.E.VICKERY,A.AGAWAL,R.D.DYER,T.SUNYER JRNL TITL DISCOVERY OF (PYRIDIN-4-YL)-2H-TETRAZOLE AS A NOVEL SCAFFOLD JRNL TITL 2 TO IDENTIFY HIGHLY SELECTIVE MATRIX METALLOPROTEINASE-13 JRNL TITL 3 INHIBITORS FOR THE TREATMENT OF OSTEOARTHRITIS. JRNL REF BIOORG.MED.CHEM.LETT. V. 20 576 2010 JRNL REFN ISSN 0960-894X JRNL PMID 20005097 JRNL DOI 10.1016/J.BMCL.2009.11.081 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 29.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 18646 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 989 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) : 1287 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2531 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.75000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -0.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.607 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2693 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1733 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3665 ; 1.153 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4218 ; 0.804 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 318 ; 5.881 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;34.673 ;24.016 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 385 ;13.564 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;25.445 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3134 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 568 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 570 ; 0.183 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1722 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1311 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1226 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 225 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 16 ; 0.110 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 16 ; 0.141 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 51 ; 0.193 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.189 ; 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): 1632 ; 0.428 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 645 ; 0.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2560 ; 0.734 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1234 ; 1.092 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1105 ; 1.590 ; 4.500 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 104 A 267 REMARK 3 ORIGIN FOR THE GROUP (A): 47.2995 30.3740 8.4734 REMARK 3 T TENSOR REMARK 3 T11: -0.1761 T22: -0.2170 REMARK 3 T33: -0.1988 T12: -0.0270 REMARK 3 T13: 0.0057 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 4.5572 L22: 2.1602 REMARK 3 L33: 2.2115 L12: 0.7086 REMARK 3 L13: -0.1800 L23: 0.9178 REMARK 3 S TENSOR REMARK 3 S11: 0.0304 S12: -0.0521 S13: 0.0358 REMARK 3 S21: 0.0525 S22: 0.0166 S23: 0.1268 REMARK 3 S31: 0.0104 S32: -0.1212 S33: -0.0471 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 104 B 267 REMARK 3 ORIGIN FOR THE GROUP (A): 76.9341 32.8918 34.4153 REMARK 3 T TENSOR REMARK 3 T11: -0.1677 T22: -0.1769 REMARK 3 T33: -0.1869 T12: 0.0329 REMARK 3 T13: -0.0191 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 4.7125 L22: 1.6643 REMARK 3 L33: 2.5333 L12: -0.5385 REMARK 3 L13: -1.0216 L23: 0.4819 REMARK 3 S TENSOR REMARK 3 S11: 0.0933 S12: 0.1420 S13: 0.0887 REMARK 3 S21: -0.1059 S22: -0.1279 S23: 0.0063 REMARK 3 S31: -0.0783 S32: -0.0176 S33: 0.0346 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3KEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : CRYSTAL REMARK 200 OPTICS : CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22451 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : 0.11200 REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS 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 (%): 56.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 5.5 MG/ML MMP-13 WITH 200 UM REMARK 280 SURROGATE INHIBITOR IN 20MM TRIS PH 8.5 AND 5 MM CACL2. REMARK 280 RESERVOIR: 1.1-1.6M LI2SO4 IN 0.1M HEPES PH 7.4-8.2. DROP RATIO: REMARK 280 5UL PROTEIN + 1 UL RESERVOIR., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K, PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 60.44150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.22850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 60.44150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.22850 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 GLY A 267 REMARK 465 PRO A 268 REMARK 465 GLY A 269 REMARK 465 ASP A 270 REMARK 465 TYR B 104 REMARK 465 ASN B 105 REMARK 465 VAL B 106 REMARK 465 PHE B 107 REMARK 465 PRO B 108 REMARK 465 ARG B 109 REMARK 465 GLY B 267 REMARK 465 PRO B 268 REMARK 465 GLY B 269 REMARK 465 ASP B 270 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 104 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 158 CG OD1 OD2 REMARK 470 MET A 253 CG SD CE REMARK 470 ASP B 158 CG OD1 OD2 REMARK 470 MET B 253 CG SD CE 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 THR A 110 105.47 89.77 REMARK 500 LYS A 170 -131.29 47.15 REMARK 500 ASP A 174 -169.98 -160.54 REMARK 500 TYR A 176 63.47 -115.59 REMARK 500 SER A 182 -154.60 59.08 REMARK 500 ASN A 194 -113.00 56.00 REMARK 500 LYS B 170 -136.57 48.59 REMARK 500 SER B 182 171.24 68.15 REMARK 500 ASN B 194 -107.28 60.45 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 905 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 128 OD2 REMARK 620 2 ASP A 203 O 149.5 REMARK 620 3 ASP A 203 OD2 109.3 63.3 REMARK 620 4 GLU A 205 O 67.5 85.2 104.4 REMARK 620 5 HOH A2003 O 147.9 58.9 64.5 143.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 904 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 147.1 REMARK 620 3 GLY A 196 O 59.4 93.3 REMARK 620 4 ASP A 198 OD1 83.0 109.4 75.9 REMARK 620 5 HOH A2011 O 69.3 81.5 59.9 135.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 118.6 REMARK 620 3 HIS A 187 NE2 137.9 89.7 REMARK 620 4 HIS A 200 ND1 102.1 94.4 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 94.1 REMARK 620 3 SER A 182 O 95.5 91.4 REMARK 620 4 LEU A 184 O 87.3 172.8 95.5 REMARK 620 5 ASP A 202 OD2 92.5 86.3 171.8 86.5 REMARK 620 6 GLU A 205 OE2 177.5 88.0 85.8 90.6 86.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 100.6 REMARK 620 3 HIS A 232 NE2 111.0 94.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 905 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2185 O REMARK 620 2 GLU B 205 O 160.4 REMARK 620 3 HOH B2005 O 128.2 50.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 904 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 162 O REMARK 620 2 ASN B 194 O 144.8 REMARK 620 3 GLY B 196 O 57.8 95.2 REMARK 620 4 ASP B 198 OD1 82.4 114.6 75.4 REMARK 620 5 HOH B2046 O 64.9 82.1 58.6 132.7 REMARK 620 6 HOH B2308 O 109.9 59.0 116.3 166.1 60.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 111.4 REMARK 620 3 HIS B 187 NE2 121.7 110.4 REMARK 620 4 HIS B 200 ND1 99.0 97.5 113.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 99.2 REMARK 620 3 SER B 182 O 83.8 82.1 REMARK 620 4 LEU B 184 O 88.6 167.1 109.2 REMARK 620 5 ASP B 202 OD2 99.8 81.1 163.1 87.4 REMARK 620 6 GLU B 205 OE2 165.8 88.8 85.7 85.9 93.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 100.5 REMARK 620 3 HIS B 232 NE2 107.5 101.7 REMARK 620 4 HOH B2235 O 107.7 103.8 131.3 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3EJ A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3EJ B 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KEC RELATED DB: PDB REMARK 900 SAME SERIES OF MMP-13 S1' INHIBITORS REMARK 900 RELATED ID: 3KEK RELATED DB: PDB REMARK 900 SAME SERIES OF MMP-13 S1' INHIBITORS DBREF 3KEJ A 104 270 UNP P45452 MMP13_HUMAN 104 270 DBREF 3KEJ B 104 270 UNP P45452 MMP13_HUMAN 104 270 SEQRES 1 A 167 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 167 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 167 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 167 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 167 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 167 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 167 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 167 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 167 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 167 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 167 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 167 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 167 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP SEQRES 1 B 167 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 B 167 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 B 167 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 B 167 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 B 167 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 B 167 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 167 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 B 167 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 B 167 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 B 167 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 B 167 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 B 167 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 B 167 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP HET ZN A 901 1 HET ZN A 902 1 HET CA A 903 1 HET CA A 904 1 HET CA A 905 1 HET 3EJ A 801 32 HET ZN B 901 1 HET ZN B 902 1 HET CA B 903 1 HET CA B 904 1 HET CA B 905 1 HET 3EJ B 801 32 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM 3EJ 4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H- HETNAM 2 3EJ TETRAZOL-2-YL)METHYL]BENZOIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 3EJ 2(C22 H17 F N6 O3) FORMUL 15 HOH *400(H2 O) HELIX 1 1 THR A 130 ASP A 147 1 18 HELIX 2 2 LEU A 216 GLY A 229 1 14 HELIX 3 3 PRO A 255 TYR A 266 1 12 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 TYR B 266 1 12 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 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 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 A 128 CA CA A 905 1555 1555 2.56 LINK O ASP A 162 CA CA A 904 1555 1555 2.90 LINK NE2 HIS A 172 ZN ZN A 902 1555 1555 2.10 LINK OD2 ASP A 174 ZN ZN A 902 1555 1555 2.08 LINK OD1 ASP A 179 CA CA A 903 1555 1555 2.46 LINK O GLY A 180 CA CA A 903 1555 1555 2.23 LINK O SER A 182 CA CA A 903 1555 1555 2.27 LINK O LEU A 184 CA CA A 903 1555 1555 2.32 LINK NE2 HIS A 187 ZN ZN A 902 1555 1555 2.49 LINK O ASN A 194 CA CA A 904 1555 1555 2.85 LINK O GLY A 196 CA CA A 904 1555 1555 3.12 LINK OD1 ASP A 198 CA CA A 904 1555 1555 2.82 LINK ND1 HIS A 200 ZN ZN A 902 1555 1555 2.05 LINK OD2 ASP A 202 CA CA A 903 1555 1555 2.31 LINK O ASP A 203 CA CA A 905 1555 1555 2.88 LINK OD2 ASP A 203 CA CA A 905 1555 1555 3.02 LINK OE2 GLU A 205 CA CA A 903 1555 1555 2.32 LINK O GLU A 205 CA CA A 905 1555 1555 2.87 LINK NE2 HIS A 222 ZN ZN A 901 1555 1555 2.14 LINK NE2 HIS A 226 ZN ZN A 901 1555 1555 2.28 LINK NE2 HIS A 232 ZN ZN A 901 1555 1555 2.00 LINK CA CA A 904 O HOH A2011 1555 1555 2.94 LINK CA CA A 905 O HOH A2003 1555 1555 3.15 LINK O HOH A2185 CA CA B 905 1555 1555 2.80 LINK O ASP B 162 CA CA B 904 1555 1555 3.04 LINK NE2 HIS B 172 ZN ZN B 902 1555 1555 1.98 LINK OD2 ASP B 174 ZN ZN B 902 1555 1555 1.86 LINK OD1 ASP B 179 CA CA B 903 1555 1555 2.56 LINK O GLY B 180 CA CA B 903 1555 1555 2.23 LINK O SER B 182 CA CA B 903 1555 1555 2.37 LINK O LEU B 184 CA CA B 903 1555 1555 2.42 LINK NE2 HIS B 187 ZN ZN B 902 1555 1555 2.01 LINK O ASN B 194 CA CA B 904 1555 1555 2.85 LINK O GLY B 196 CA CA B 904 1555 1555 2.93 LINK OD1 ASP B 198 CA CA B 904 1555 1555 2.55 LINK ND1 HIS B 200 ZN ZN B 902 1555 1555 2.02 LINK OD2 ASP B 202 CA CA B 903 1555 1555 2.36 LINK OE2 GLU B 205 CA CA B 903 1555 1555 2.26 LINK O GLU B 205 CA CA B 905 1555 1555 2.89 LINK NE2 HIS B 222 ZN ZN B 901 1555 1555 2.16 LINK NE2 HIS B 226 ZN ZN B 901 1555 1555 2.16 LINK NE2 HIS B 232 ZN ZN B 901 1555 1555 2.08 LINK ZN ZN B 901 O HOH B2235 1555 1555 2.21 LINK CA CA B 904 O HOH B2046 1555 1555 3.15 LINK CA CA B 904 O HOH B2308 1555 1555 3.01 LINK CA CA B 905 O HOH B2005 1555 1555 2.91 SITE 1 AC1 3 HIS A 222 HIS A 226 HIS A 232 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 ALA A 161 ASP A 162 ASN A 194 GLY A 196 SITE 2 AC4 6 ASP A 198 HOH A2011 SITE 1 AC5 4 THR A 126 ASP A 128 ASP A 203 GLU A 205 SITE 1 AC6 20 LYS A 140 ASN A 215 PHE A 217 LEU A 218 SITE 2 AC6 20 HIS A 222 ALA A 238 LEU A 239 PHE A 241 SITE 3 AC6 20 PRO A 242 ILE A 243 TYR A 244 THR A 245 SITE 4 AC6 20 TYR A 246 THR A 247 GLY A 248 LYS A 249 SITE 5 AC6 20 SER A 250 PHE A 252 HOH A2102 HOH A2322 SITE 1 AC7 4 HIS B 222 HIS B 226 HIS B 232 HOH B2235 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 ALA B 161 ASP B 162 ASN B 194 GLY B 196 SITE 2 BC1 6 ASP B 198 HOH B2308 SITE 1 BC2 5 HOH A2185 ASP B 128 GLU B 205 THR B 206 SITE 2 BC2 5 HOH B2005 SITE 1 BC3 19 LYS B 140 ASN B 215 PHE B 217 LEU B 218 SITE 2 BC3 19 HIS B 222 ALA B 238 LEU B 239 PHE B 241 SITE 3 BC3 19 PRO B 242 ILE B 243 TYR B 244 THR B 245 SITE 4 BC3 19 THR B 247 GLY B 248 LYS B 249 HIS B 251 SITE 5 BC3 19 PHE B 252 HOH B2145 HOH B2240 CRYST1 120.883 96.457 36.638 90.00 90.00 90.00 P 21 21 2 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 0.008272 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027294 0.00000