PDB Short entry for 1YOU HEADER HYDROLASE 28-JAN-05 1YOU TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH A TITLE 2 POTENT PYRIMIDINETRIONE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MMP-13 CATALYTIC DOMAIN; COMPND 5 SYNONYM: MATRIX METALLOPROTEINASE-13, MMP-13; COMPND 6 EC: 3.4.24.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MMP13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, METALLOPROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR J.PANDIT REVDAT 4 23-AUG-23 1YOU 1 REMARK LINK REVDAT 3 13-JUL-11 1YOU 1 VERSN REVDAT 2 24-FEB-09 1YOU 1 VERSN REVDAT 1 15-MAR-05 1YOU 0 JRNL AUTH J.A.BLAGG,M.C.NOE,L.A.WOLF-GOUVEIA,L.A.REITER,E.R.LAIRD, JRNL AUTH 2 S.P.CHANG,D.E.DANLEY,J.T.DOWNS,N.C.ELLIOTT,J.D.ESKRA, JRNL AUTH 3 R.J.GRIFFITHS,J.R.HARDINK,A.I.HAUGETO,C.S.JONES,J.L.LIRAS, JRNL AUTH 4 L.L.LOPRESTI-MORROW,P.G.MITCHELL,J.PANDIT,R.P.ROBINSON, JRNL AUTH 5 C.SUBRAMANYAM,M.L.VAUGHN-BOWSER,S.A.YOCUM JRNL TITL POTENT PYRIMIDINETRIONE-BASED INHIBITORS OF MMP-13 WITH JRNL TITL 2 ENHANCED SELECTIVITY OVER MMP-14. JRNL REF BIOORG.MED.CHEM.LETT. V. 15 1807 2005 JRNL REFN ISSN 0960-894X JRNL PMID 15780611 JRNL DOI 10.1016/J.BMCL.2005.02.038 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 12847 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1080 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) : 664 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2637 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : 1.07000 REMARK 3 B33 (A**2) : -0.83000 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): 0.600 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.327 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.881 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.847 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2806 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3822 ; 2.064 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 7.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;38.600 ;23.969 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;19.781 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;14.044 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2224 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1222 ; 0.233 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1811 ; 0.321 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 89 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 18 ; 0.140 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 68 ; 0.317 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.219 ; 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): 1702 ; 1.042 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2659 ; 1.726 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1308 ; 2.696 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1163 ; 3.485 ; 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 : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 112 A 173 4 REMARK 3 1 B 112 B 173 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 510 ; 0.35 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 510 ; 1.36 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 176 A 247 4 REMARK 3 1 B 176 B 247 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 556 ; 0.31 ; 0.50 REMARK 3 MEDIUM THERMAL 2 A (A**2): 556 ; 1.50 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 252 A 268 4 REMARK 3 1 B 252 B 268 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 3 A (A): 129 ; 0.36 ; 0.50 REMARK 3 MEDIUM THERMAL 3 A (A**2): 129 ; 1.68 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1YOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031762. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15989 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 830C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP 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 40.54450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.11150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.54450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.11150 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: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -298.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 81.08900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 108.22300 REMARK 350 BIOMT3 2 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 B 269 REMARK 465 ASP B 270 REMARK 465 GLU B 271 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 SER A 250 OG REMARK 470 MET A 253 CG SD CE REMARK 470 LYS B 249 CB CG CD CE NZ REMARK 470 SER B 250 OG REMARK 470 HIS B 251 CB CG ND1 CD2 CE1 NE2 REMARK 470 MET B 253 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE A 175 OH TYR B 195 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 193 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO B 108 C - N - CA ANGL. DEV. = 10.5 DEGREES 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 ARG A 109 157.56 77.96 REMARK 500 THR A 110 86.52 -162.23 REMARK 500 LYS A 170 -141.35 49.20 REMARK 500 PHE A 175 19.80 57.72 REMARK 500 SER A 182 -164.06 63.79 REMARK 500 ASN A 194 -112.35 57.91 REMARK 500 ASP A 202 101.54 -57.76 REMARK 500 SER A 210 -154.97 -129.18 REMARK 500 PRO A 242 39.14 -75.16 REMARK 500 LYS A 249 -65.37 -20.65 REMARK 500 ASN B 105 117.53 88.41 REMARK 500 ARG B 109 -46.86 6.85 REMARK 500 THR B 110 150.28 178.18 REMARK 500 VAL B 144 -48.83 -28.85 REMARK 500 LYS B 170 -134.49 59.08 REMARK 500 TYR B 176 64.63 -115.03 REMARK 500 SER B 182 -164.87 54.97 REMARK 500 ASN B 194 -109.29 72.69 REMARK 500 SER B 210 -110.68 -122.64 REMARK 500 PRO B 242 20.54 -77.49 REMARK 500 THR B 247 -43.70 -147.90 REMARK 500 SER B 250 -89.03 3.68 REMARK 500 HIS B 251 55.40 -104.07 REMARK 500 LEU B 254 113.46 -36.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 108 ARG B 109 137.62 REMARK 500 LYS B 249 SER B 250 147.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 114.8 REMARK 620 3 HIS A 187 NE2 113.3 111.4 REMARK 620 4 HIS A 200 ND1 104.3 97.9 113.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 79.3 REMARK 620 3 SER A 182 O 85.9 86.5 REMARK 620 4 LEU A 184 O 96.3 174.1 89.3 REMARK 620 5 ASP A 202 OD2 91.5 91.0 176.7 93.0 REMARK 620 6 GLU A 205 OE2 175.7 96.6 92.5 87.7 89.9 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 102.7 REMARK 620 3 HIS A 232 NE2 112.1 82.4 REMARK 620 4 PFD A 998 N9 107.8 124.1 124.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 172 NE2 REMARK 620 2 ASP B 174 OD2 112.2 REMARK 620 3 HIS B 187 NE2 123.0 108.9 REMARK 620 4 HIS B 200 ND1 90.8 106.3 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 179 OD1 REMARK 620 2 GLY B 180 O 96.7 REMARK 620 3 SER B 182 O 88.4 89.6 REMARK 620 4 LEU B 184 O 76.5 173.1 89.3 REMARK 620 5 ASP B 202 OD2 101.0 85.5 169.9 96.6 REMARK 620 6 GLU B 205 OE2 161.9 99.7 84.1 87.0 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 222 NE2 REMARK 620 2 HIS B 226 NE2 101.4 REMARK 620 3 HIS B 232 NE2 109.6 95.1 REMARK 620 4 PFD B 999 N9 105.4 134.6 109.2 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 ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFD A 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFD B 999 DBREF 1YOU A 104 271 UNP P45452 MMP13_HUMAN 104 271 DBREF 1YOU B 104 271 UNP P45452 MMP13_HUMAN 104 271 SEQRES 1 A 168 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 168 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 168 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 168 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 168 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 168 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 168 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 168 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 168 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 168 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 168 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 168 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 168 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU SEQRES 1 B 168 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 B 168 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 B 168 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 B 168 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 B 168 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 B 168 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 168 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 B 168 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 B 168 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 B 168 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 B 168 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 B 168 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 B 168 GLN GLY ILE GLN SER LEU TYR GLY PRO GLY ASP GLU HET ZN A 301 1 HET ZN A 302 1 HET CA A 401 1 HET SO4 A 501 5 HET SO4 A 502 5 HET PFD A 998 29 HET ZN B 303 1 HET ZN B 304 1 HET CA B 403 1 HET SO4 B 503 5 HET PFD B 999 29 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM PFD 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY) HETNAM 2 PFD PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 2(CA 2+) FORMUL 6 SO4 3(O4 S 2-) FORMUL 8 PFD 2(C20 H19 F N2 O6) FORMUL 14 HOH *17(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 GLY A 248 PHE A 252 5 5 HELIX 4 4 PRO A 255 GLY A 267 1 13 HELIX 5 5 THR B 130 ASP B 147 1 18 HELIX 6 6 LEU B 216 LEU B 228 1 13 HELIX 7 7 GLY B 248 PHE B 252 5 5 HELIX 8 8 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 THR A 154 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 LEU B 118 O ASN B 152 SHEET 3 C 5 ILE B 163 GLY B 168 1 O ILE B 165 N ARG B 121 SHEET 4 C 5 ALA B 199 ASP B 202 1 O PHE B 201 N GLY B 168 SHEET 5 C 5 ALA B 186 ALA B 188 -1 N HIS B 187 O HIS B 200 SHEET 1 D 2 TRP B 207 THR B 208 0 SHEET 2 D 2 TYR B 214 ASN B 215 1 O TYR B 214 N THR B 208 LINK NE2 HIS A 172 ZN ZN A 302 1555 1555 2.06 LINK OD2 ASP A 174 ZN ZN A 302 1555 1555 1.99 LINK OD1 ASP A 179 CA CA A 401 1555 1555 2.33 LINK O GLY A 180 CA CA A 401 1555 1555 2.29 LINK O SER A 182 CA CA A 401 1555 1555 2.31 LINK O LEU A 184 CA CA A 401 1555 1555 2.19 LINK NE2 HIS A 187 ZN ZN A 302 1555 1555 2.06 LINK ND1 HIS A 200 ZN ZN A 302 1555 1555 1.90 LINK OD2 ASP A 202 CA CA A 401 1555 1555 2.39 LINK OE2 GLU A 205 CA CA A 401 1555 1555 2.21 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.11 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.41 LINK NE2 HIS A 232 ZN ZN A 301 1555 1555 2.09 LINK ZN ZN A 301 N9 PFD A 998 1555 1555 2.11 LINK NE2 HIS B 172 ZN ZN B 304 1555 1555 1.89 LINK OD2 ASP B 174 ZN ZN B 304 1555 1555 1.93 LINK OD1 ASP B 179 CA CA B 403 1555 1555 2.26 LINK O GLY B 180 CA CA B 403 1555 1555 2.23 LINK O SER B 182 CA CA B 403 1555 1555 2.47 LINK O LEU B 184 CA CA B 403 1555 1555 2.45 LINK NE2 HIS B 187 ZN ZN B 304 1555 1555 2.12 LINK ND1 HIS B 200 ZN ZN B 304 1555 1555 2.05 LINK OD2 ASP B 202 CA CA B 403 1555 1555 2.21 LINK OE2 GLU B 205 CA CA B 403 1555 1555 2.20 LINK NE2 HIS B 222 ZN ZN B 303 1555 1555 2.28 LINK NE2 HIS B 226 ZN ZN B 303 1555 1555 2.03 LINK NE2 HIS B 232 ZN ZN B 303 1555 1555 2.02 LINK ZN ZN B 303 N9 PFD B 999 1555 1555 2.10 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 PFD A 998 SITE 1 AC2 4 HIS A 172 ASP A 174 HIS A 187 HIS A 200 SITE 1 AC3 4 HIS B 222 HIS B 226 HIS B 232 PFD B 999 SITE 1 AC4 4 HIS B 172 ASP B 174 HIS B 187 HIS B 200 SITE 1 AC5 6 ASP A 179 GLY A 180 SER A 182 LEU A 184 SITE 2 AC5 6 ASP A 202 GLU A 205 SITE 1 AC6 6 ASP B 179 GLY B 180 SER B 182 LEU B 184 SITE 2 AC6 6 ASP B 202 GLU B 205 SITE 1 AC7 4 THR A 130 HIS A 131 THR B 130 HIS B 131 SITE 1 AC8 3 LYS A 115 MET A 116 ASN A 117 SITE 1 AC9 4 LYS B 115 MET B 116 ASN B 117 LYS B 234 SITE 1 BC1 14 LEU A 184 LEU A 185 ALA A 186 HIS A 222 SITE 2 BC1 14 GLU A 223 HIS A 226 HIS A 232 LEU A 239 SITE 3 BC1 14 PHE A 241 PRO A 242 ILE A 243 TYR A 244 SITE 4 BC1 14 THR A 245 ZN A 301 SITE 1 BC2 15 LEU B 184 LEU B 185 ALA B 186 VAL B 219 SITE 2 BC2 15 HIS B 222 GLU B 223 HIS B 226 HIS B 232 SITE 3 BC2 15 LEU B 239 PHE B 241 PRO B 242 ILE B 243 SITE 4 BC2 15 TYR B 244 THR B 245 ZN B 303 CRYST1 81.089 108.223 36.035 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 0.012332 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027751 0.00000