HEADER HYDROLASE/HYDROLASE INHIBITOR 11-NOV-06 2E2D TITLE FLEXIBILITY AND VARIABILITY OF TIMP BINDING: X-RAY STRUCTURE OF THE TITLE 2 COMPLEX BETWEEN COLLAGENASE-3/MMP-13 AND TIMP-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX METALLOPEPTIDASE 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: MMP-13; COLLAGENASE-3; COMPND 6 EC: 3.4.24.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: METALLOPROTEINASE INHIBITOR 2; COMPND 10 CHAIN: C; COMPND 11 SYNONYM: TIMP-2; TISSUE INHIBITOR OF METALLOPROTEINASES 2; COMPND 12 COLLAGENASE INHIBITOR; COMPND 13 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_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 11 ORGANISM_COMMON: CATTLE; SOURCE 12 ORGANISM_TAXID: 9913; SOURCE 13 GENE: TIMP2; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS MATRIX METALLOPROTEINASE-MMP; COLLAGENASE; TISSUE INHIBITOR OF KEYWDS 2 METALLOPROTEINASES-TIMP; COMPLEX, FLEXIBILITY, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.MASKOS,R.LANG,H.TSCHESCHE,W.BODE REVDAT 4 06-NOV-24 2E2D 1 REMARK REVDAT 3 23-AUG-23 2E2D 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2E2D 1 VERSN REVDAT 1 13-MAR-07 2E2D 0 JRNL AUTH K.MASKOS,R.LANG,H.TSCHESCHE,W.BODE JRNL TITL FLEXIBILITY AND VARIABILITY OF TIMP BINDING: X-RAY STRUCTURE JRNL TITL 2 OF THE COMPLEX BETWEEN COLLAGENASE-3/MMP-13 AND TIMP-2 JRNL REF J.MOL.BIOL. V. 366 1222 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17196980 JRNL DOI 10.1016/J.JMB.2006.11.072 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34445 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1800 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2725 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 323 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.48000 REMARK 3 B22 (A**2) : 1.48000 REMARK 3 B33 (A**2) : -2.21000 REMARK 3 B12 (A**2) : 0.74000 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.170 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2770 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2374 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3758 ; 1.626 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5559 ; 0.795 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 4.698 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 483 ;18.653 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3100 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 570 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 688 ; 0.278 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2447 ; 0.222 ; 0.300 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): 377 ; 0.256 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 5 ; 0.177 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 17 ; 0.376 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.392 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.428 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.171 ; 0.500 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): 1701 ; 0.898 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2737 ; 1.653 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1069 ; 2.187 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1021 ; 3.484 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2E2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000026137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-99; 26-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; MPG/DESY, REMARK 200 HAMBURG REMARK 200 BEAMLINE : NULL; BW6 REMARK 200 X-RAY GENERATOR MODEL : RIGAKU; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.0503 REMARK 200 MONOCHROMATOR : GRAPHITE; NULL REMARK 200 OPTICS : MIRRORS; MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; MAR REMARK 200 SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36318 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 23.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 1.0 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : 0.49800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.031 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 830C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 200 MM MAGNESIUM ACETATE, REMARK 280 20 % PEG 8000, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 120.91667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.45833 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.68750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.22917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 151.14583 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 248 REMARK 475 LYS A 249 REMARK 475 SER A 250 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS C 1022 CE NZ REMARK 480 LYS C 1081 CG CD CE NZ REMARK 480 LYS C 1169 CD CE NZ 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 SER A 250 N HIS A 251 1.72 REMARK 500 NH2 ARG A 109 OG SER A 264 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 CD1 ILE A 160 O THR C 1153 6654 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 250 C HIS A 251 N -0.392 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 ASP A 203 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 SER A 250 CA - C - N ANGL. DEV. = 19.2 DEGREES REMARK 500 SER A 250 O - C - N ANGL. DEV. = -19.2 DEGREES REMARK 500 ASP C1034 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP C1102 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP C1108 CB - CG - OD2 ANGL. DEV. = 5.6 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 PRO A 108 105.02 -33.57 REMARK 500 LEU A 111 65.82 -100.70 REMARK 500 LYS A 170 -126.22 59.74 REMARK 500 SER A 182 -168.35 66.72 REMARK 500 ASN A 194 -122.72 34.83 REMARK 500 SER A 210 -159.49 -138.04 REMARK 500 SER A 250 -18.31 -152.65 REMARK 500 CYS C1072 41.34 72.19 REMARK 500 GLU C1091 -152.99 -111.03 REMARK 500 ASN C1093 111.72 -32.06 REMARK 500 HIS C1120 -29.64 -159.34 REMARK 500 LYS C1155 71.76 -109.84 REMARK 500 ASN C1158 45.47 -99.58 REMARK 500 SER C1171 -72.90 -69.31 REMARK 500 SER C1174 -98.28 -97.00 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 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 O REMARK 620 2 ASN A 194 O 172.5 REMARK 620 3 GLY A 196 O 96.1 87.4 REMARK 620 4 ASP A 198 OD1 92.8 93.7 91.5 REMARK 620 5 HOH A 537 O 86.0 89.2 167.1 101.1 REMARK 620 6 HOH A 551 O 89.2 84.8 81.0 172.3 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 172 NE2 REMARK 620 2 ASP A 174 OD2 100.6 REMARK 620 3 HIS A 187 NE2 123.4 117.7 REMARK 620 4 HIS A 200 ND1 103.1 95.0 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 GLY A 180 O 86.1 REMARK 620 3 SER A 182 O 87.9 90.2 REMARK 620 4 LEU A 184 O 94.5 176.3 93.5 REMARK 620 5 ASP A 202 OD2 94.7 86.9 175.9 89.4 REMARK 620 6 GLU A 205 OE2 174.2 91.6 86.8 88.1 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 NE2 REMARK 620 2 HIS A 226 NE2 93.2 REMARK 620 3 HIS A 232 NE2 106.9 93.2 REMARK 620 4 CYS C1001 N 129.7 90.2 123.0 REMARK 620 5 CYS C1001 O 87.8 169.6 96.5 81.3 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BQQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MT1-MMP-TIMP-2 COMPLEX REMARK 900 RELATED ID: 1BUV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MT1-MMP-TIMP-2 COMPLEX REMARK 900 RELATED ID: 1BR9 RELATED DB: PDB REMARK 900 HUMAN TISSUE INHIBITOR OF METALLOPROTEINASE-2 REMARK 900 RELATED ID: 830C RELATED DB: PDB REMARK 900 COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID DBREF 2E2D A 104 268 UNP P45452 MMP13_HUMAN 104 268 DBREF 2E2D C 1002 1180 UNP P16368 TIMP2_BOVIN 28 206 SEQADV 2E2D CYS C 1001 UNP P16368 CLONING ARTIFACT SEQRES 1 A 165 TYR ASN VAL PHE PRO ARG THR LEU LYS TRP SER LYS MET SEQRES 2 A 165 ASN LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP MET SEQRES 3 A 165 THR HIS SER GLU VAL GLU LYS ALA PHE LYS LYS ALA PHE SEQRES 4 A 165 LYS VAL TRP SER ASP VAL THR PRO LEU ASN PHE THR ARG SEQRES 5 A 165 LEU HIS ASP GLY ILE ALA ASP ILE MET ILE SER PHE GLY SEQRES 6 A 165 ILE LYS GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 165 SER GLY LEU LEU ALA HIS ALA PHE PRO PRO GLY PRO ASN SEQRES 8 A 165 TYR GLY GLY ASP ALA HIS PHE ASP ASP ASP GLU THR TRP SEQRES 9 A 165 THR SER SER SER LYS GLY TYR ASN LEU PHE LEU VAL ALA SEQRES 10 A 165 ALA HIS GLU PHE GLY HIS SER LEU GLY LEU ASP HIS SER SEQRES 11 A 165 LYS ASP PRO GLY ALA LEU MET PHE PRO ILE TYR THR TYR SEQRES 12 A 165 THR GLY LYS SER HIS PHE MET LEU PRO ASP ASP ASP VAL SEQRES 13 A 165 GLN GLY ILE GLN SER LEU TYR GLY PRO SEQRES 1 C 180 CYS SER CYS SER PRO VAL HIS PRO GLN GLN ALA PHE CYS SEQRES 2 C 180 ASN ALA ASP ILE VAL ILE ARG ALA LYS ALA VAL ASN LYS SEQRES 3 C 180 LYS GLU VAL ASP SER GLY ASN ASP ILE TYR GLY ASN PRO SEQRES 4 C 180 ILE LYS ARG ILE GLN TYR GLU ILE LYS GLN ILE LYS MET SEQRES 5 C 180 PHE LYS GLY PRO ASP GLN ASP ILE GLU PHE ILE TYR THR SEQRES 6 C 180 ALA PRO ALA ALA ALA VAL CYS GLY VAL SER LEU ASP ILE SEQRES 7 C 180 GLY GLY LYS LYS GLU TYR LEU ILE ALA GLY LYS ALA GLU SEQRES 8 C 180 GLY ASN GLY ASN MET HIS ILE THR LEU CYS ASP PHE ILE SEQRES 9 C 180 VAL PRO TRP ASP THR LEU SER ALA THR GLN LYS LYS SER SEQRES 10 C 180 LEU ASN HIS ARG TYR GLN MET GLY CYS GLU CYS LYS ILE SEQRES 11 C 180 THR ARG CYS PRO MET ILE PRO CYS TYR ILE SER SER PRO SEQRES 12 C 180 ASP GLU CYS LEU TRP MET ASP TRP VAL THR GLU LYS ASN SEQRES 13 C 180 ILE ASN GLY HIS GLN ALA LYS PHE PHE ALA CYS ILE LYS SEQRES 14 C 180 ARG SER ASP GLY SER CYS ALA TRP TYR ARG GLY HET ZN A 500 1 HET ZN A 501 1 HET CA A 502 1 HET CA A 503 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *323(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 HIS C 1007 ALA C 1015 1 9 HELIX 5 5 ALA C 1068 CYS C 1072 5 5 HELIX 6 6 ASP C 1108 LEU C 1110 5 3 HELIX 7 7 SER C 1111 LEU C 1118 1 8 HELIX 8 8 HIS C 1120 CYS C 1126 1 7 HELIX 9 9 MET C 1149 GLU C 1154 1 6 HELIX 10 10 GLY C 1159 PHE C 1165 1 7 SHEET 1 A 6 ASN A 152 ARG A 155 0 SHEET 2 A 6 ASN A 117 ILE A 122 1 N LEU A 118 O ASN A 152 SHEET 3 A 6 ILE A 163 GLY A 168 1 O ILE A 163 N THR A 119 SHEET 4 A 6 ALA A 199 ASP A 202 1 O PHE A 201 N GLY A 168 SHEET 5 A 6 LEU A 184 ALA A 188 -1 N HIS A 187 O HIS A 200 SHEET 6 A 6 SER C1002 CYS C1003 -1 O SER C1002 N LEU A 185 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 7 ILE C1104 PRO C1106 0 SHEET 2 C 7 GLU C1083 ALA C1090 -1 N LEU C1085 O VAL C1105 SHEET 3 C 7 ASN C1095 HIS C1097 -1 O HIS C1097 N LYS C1089 SHEET 4 C 7 PHE C1062 THR C1065 1 N TYR C1064 O MET C1096 SHEET 5 C 7 PRO C1039 LYS C1054 -1 N TYR C1045 O ILE C1063 SHEET 6 C 7 ILE C1017 ASN C1033 -1 N GLY C1032 O ILE C1040 SHEET 7 C 7 GLU C1083 ALA C1090 -1 O TYR C1084 N ALA C1021 SHEET 1 D 2 LYS C1129 ARG C1132 0 SHEET 2 D 2 GLU C1145 TRP C1148 1 O TRP C1148 N THR C1131 SHEET 1 E 2 ALA C1166 LYS C1169 0 SHEET 2 E 2 CYS C1175 TYR C1178 -1 O TYR C1178 N ALA C1166 SSBOND 1 CYS C 1001 CYS C 1072 1555 1555 2.03 SSBOND 2 CYS C 1003 CYS C 1101 1555 1555 1.99 SSBOND 3 CYS C 1013 CYS C 1126 1555 1555 2.03 SSBOND 4 CYS C 1128 CYS C 1175 1555 1555 2.06 SSBOND 5 CYS C 1133 CYS C 1138 1555 1555 2.03 SSBOND 6 CYS C 1146 CYS C 1167 1555 1555 2.05 LINK O ASP A 162 CA CA A 503 1555 1555 2.23 LINK NE2 HIS A 172 ZN ZN A 501 1555 1555 1.91 LINK OD2 ASP A 174 ZN ZN A 501 1555 1555 2.01 LINK OD1 ASP A 179 CA CA A 502 1555 1555 2.31 LINK O GLY A 180 CA CA A 502 1555 1555 2.28 LINK O SER A 182 CA CA A 502 1555 1555 2.28 LINK O LEU A 184 CA CA A 502 1555 1555 2.34 LINK NE2 HIS A 187 ZN ZN A 501 1555 1555 1.96 LINK O ASN A 194 CA CA A 503 1555 1555 2.38 LINK O GLY A 196 CA CA A 503 1555 1555 2.33 LINK OD1 ASP A 198 CA CA A 503 1555 1555 2.44 LINK ND1 HIS A 200 ZN ZN A 501 1555 1555 1.96 LINK OD2 ASP A 202 CA CA A 502 1555 1555 2.19 LINK OE2 GLU A 205 CA CA A 502 1555 1555 2.21 LINK NE2 HIS A 222 ZN ZN A 500 1555 1555 2.05 LINK NE2 HIS A 226 ZN ZN A 500 1555 1555 2.18 LINK NE2 HIS A 232 ZN ZN A 500 1555 1555 1.93 LINK ZN ZN A 500 N CYS C1001 1555 1555 1.99 LINK ZN ZN A 500 O CYS C1001 1555 1555 2.36 LINK CA CA A 503 O HOH A 537 1555 1555 2.41 LINK CA CA A 503 O HOH A 551 1555 1555 2.44 CISPEP 1 ILE C 1136 PRO C 1137 0 0.07 SITE 1 AC1 4 HIS A 222 HIS A 226 HIS A 232 CYS C1001 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 537 HOH A 551 CRYST1 72.526 72.526 181.375 90.00 90.00 120.00 P 65 6 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 0.013788 0.007961 0.000000 0.00000 SCALE2 0.000000 0.015921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005513 0.00000