PDB Short entry for 4JA1 HEADER HYDROLASE/HYDROLASE INHIBITOR 18-FEB-13 4JA1 TITLE STRUCTURE OF MMP3 COMPLEXED WITH A PLATINUM-BASED INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMELYSIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: SL-1, MATRIX METALLOPROTEINASE-3, MMP-3, TRANSIN-1; COMPND 6 EC: 3.4.24.17; 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: MMP3, STMY1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MATRIX METALLOPROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.BELVISO,F.ARNESANO,V.CALDERONE,R.CALIANDRO,G.NATILE,D.SILIQI REVDAT 6 20-SEP-23 4JA1 1 REMARK LINK REVDAT 5 05-JUN-13 4JA1 1 JRNL REVDAT 4 29-MAY-13 4JA1 1 HEADER KEYWDS REVDAT 3 22-MAY-13 4JA1 1 JRNL REVDAT 2 15-MAY-13 4JA1 1 JRNL REVDAT 1 27-FEB-13 4JA1 0 JRNL AUTH B.D.BELVISO,R.CALIANDRO,D.SILIQI,V.CALDERONE,F.ARNESANO, JRNL AUTH 2 G.NATILE JRNL TITL STRUCTURE OF MATRIX METALLOPROTEINASE-3 WITH A JRNL TITL 2 PLATINUM-BASED INHIBITOR. JRNL REF CHEM.COMMUN.(CAMB.) V. 49 5492 2013 JRNL REFN ISSN 1359-7345 JRNL PMID 23660647 JRNL DOI 10.1039/C3CC41278D REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20446 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2136 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1561 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2663 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4JA1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 34.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: ILMILIONE REMARK 200 STARTING MODEL: PDB ENTRY 1SLN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 7-15MG/ML, 25-30% (W/V) PEG REMARK 280 8000, 10 MM CACL2, 100 MM TRIS, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.05950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.02400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.80750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.02400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.05950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.80750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ASP A 251 REMARK 465 SER A 252 REMARK 465 PRO A 253 REMARK 465 GLU A 254 REMARK 465 THR A 255 REMARK 465 PHE B 83 REMARK 465 ARG B 84 REMARK 465 THR B 85 REMARK 465 PHE B 86 REMARK 465 PRO B 87 REMARK 465 GLY B 88 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 OE2 GLU A 139 PT PT A 306 1.63 REMARK 500 OE2 GLU A 125 O HOH A 447 1.76 REMARK 500 CE MET A 143 CL CL A 307 1.76 REMARK 500 CE MET B 143 CL CL B 309 1.96 REMARK 500 OE1 GLU B 125 O HOH B 401 2.17 REMARK 500 O HIS A 224 N LEU A 226 2.19 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 149 -137.50 41.04 REMARK 500 HIS A 151 20.52 -146.32 REMARK 500 ASP A 153 -159.35 -136.95 REMARK 500 ASN A 162 -119.48 52.08 REMARK 500 ASP A 189 -146.27 -116.75 REMARK 500 SER A 225 70.26 -45.72 REMARK 500 LEU A 226 -95.81 37.72 REMARK 500 THR A 227 -159.54 -86.63 REMARK 500 ASP A 228 95.78 42.67 REMARK 500 ARG B 149 -129.93 44.92 REMARK 500 HIS B 151 16.26 -146.49 REMARK 500 ASP B 153 -166.36 -120.77 REMARK 500 ASN B 162 -125.95 52.20 REMARK 500 ASP B 189 -156.53 -109.14 REMARK 500 PRO B 221 49.01 -76.63 REMARK 500 ASP B 228 47.79 88.37 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 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 107 OD2 REMARK 620 2 ASP A 107 OD1 49.9 REMARK 620 3 ASP A 182 O 147.9 156.8 REMARK 620 4 ASP A 182 OD1 85.3 89.2 80.5 REMARK 620 5 GLU A 184 O 75.5 121.3 81.8 108.2 REMARK 620 6 HOH A 405 O 128.7 79.3 79.6 88.0 153.0 REMARK 620 7 HOH A 415 O 100.1 87.8 98.6 169.8 81.7 81.9 REMARK 620 N 1 2 3 4 5 6 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 141 O REMARK 620 2 GLY A 173 O 166.3 REMARK 620 3 ASN A 175 O 103.4 88.6 REMARK 620 4 ASP A 177 OD1 87.1 99.4 91.3 REMARK 620 5 HOH A 401 O 82.4 93.3 80.6 164.8 REMARK 620 6 HOH A 443 O 91.9 75.6 164.0 94.2 97.1 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 151 NE2 REMARK 620 2 ASP A 153 OD2 110.3 REMARK 620 3 HIS A 166 NE2 120.9 105.5 REMARK 620 4 HIS A 179 ND1 104.3 99.9 114.1 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 158 OD1 REMARK 620 2 GLY A 159 O 87.0 REMARK 620 3 GLY A 161 O 91.4 94.8 REMARK 620 4 VAL A 163 O 90.6 177.3 84.2 REMARK 620 5 ASP A 181 OD2 89.3 85.9 179.0 95.1 REMARK 620 6 GLU A 184 OE2 178.7 94.1 87.7 88.3 91.6 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 201 NE2 REMARK 620 2 HIS A 205 NE2 101.0 REMARK 620 3 HIS A 211 NE2 119.3 109.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 107 OD2 REMARK 620 2 ASP B 107 OD1 51.1 REMARK 620 3 ASP B 182 O 146.3 156.2 REMARK 620 4 ASP B 182 OD1 87.7 95.0 74.6 REMARK 620 5 GLU B 184 O 76.7 121.6 82.2 108.7 REMARK 620 6 HOH B 444 O 97.9 79.7 105.7 167.0 84.1 REMARK 620 7 HOH B 454 O 128.9 79.6 78.1 83.8 152.9 83.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PT B 307 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 139 OE1 REMARK 620 2 HOH B 440 O 64.2 REMARK 620 N 1 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 141 O REMARK 620 2 GLY B 173 O 171.7 REMARK 620 3 ASN B 175 O 100.0 87.8 REMARK 620 4 ASP B 177 OD1 87.6 95.6 89.3 REMARK 620 5 HOH B 402 O 92.6 79.4 166.7 95.4 REMARK 620 6 HOH B 404 O 87.1 91.4 79.9 167.0 96.7 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 151 NE2 REMARK 620 2 ASP B 153 OD2 108.9 REMARK 620 3 HIS B 166 NE2 124.0 104.5 REMARK 620 4 HIS B 179 ND1 104.7 99.3 112.8 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 158 OD1 REMARK 620 2 GLY B 159 O 86.1 REMARK 620 3 GLY B 161 O 87.4 83.7 REMARK 620 4 VAL B 163 O 92.8 175.9 92.3 REMARK 620 5 ASP B 181 OD2 93.1 88.4 172.1 95.6 REMARK 620 6 GLU B 184 OE2 170.6 89.5 83.9 91.0 95.1 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 201 NE2 REMARK 620 2 HIS B 205 NE2 95.0 REMARK 620 3 HIS B 211 NE2 111.3 99.4 REMARK 620 4 NGH B 306 O5 115.9 148.8 74.4 REMARK 620 5 NGH B 306 O4 107.0 97.4 136.3 70.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PT B 308 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 224 ND1 REMARK 620 2 HOH B 420 O 172.7 REMARK 620 N 1 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 CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PT A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NGH B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PT B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PT B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 311 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DPE RELATED DB: PDB DBREF 4JA1 A 83 255 UNP P08254 MMP3_HUMAN 100 272 DBREF 4JA1 B 83 255 UNP P08254 MMP3_HUMAN 100 272 SEQRES 1 A 173 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 A 173 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 A 173 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 A 173 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 A 173 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 A 173 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 173 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 A 173 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 A 173 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 A 173 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 A 173 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 A 173 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 A 173 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 A 173 SER PRO GLU THR SEQRES 1 B 173 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 B 173 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 B 173 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 B 173 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 B 173 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 B 173 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 B 173 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 B 173 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 B 173 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 B 173 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 B 173 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 B 173 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 B 173 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 14 B 173 SER PRO GLU THR HET ZN A 301 1 HET ZN A 302 1 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HET PT A 306 1 HET CL A 307 1 HET ZN B 301 1 HET ZN B 302 1 HET CA B 303 1 HET CA B 304 1 HET CA B 305 1 HET NGH B 306 21 HET PT B 307 1 HET PT B 308 1 HET CL B 309 1 HET CL B 310 1 HET CL B 311 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM PT PLATINUM (II) ION HETNAM CL CHLORIDE ION HETNAM NGH N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC HETNAM 2 NGH ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA 6(CA 2+) FORMUL 8 PT 3(PT 2+) FORMUL 9 CL 4(CL 1-) FORMUL 15 NGH C13 H20 N2 O5 S FORMUL 21 HOH *108(H2 O) HELIX 1 1 PRO A 109 GLU A 126 1 18 HELIX 2 2 LEU A 195 LEU A 207 1 13 HELIX 3 3 ASP A 228 PHE A 232 5 5 HELIX 4 4 SER A 235 GLY A 247 1 13 HELIX 5 5 PRO B 109 GLU B 126 1 18 HELIX 6 6 LEU B 195 LEU B 207 1 13 HELIX 7 7 SER B 235 GLY B 247 1 13 SHEET 1 A 5 THR A 131 ARG A 134 0 SHEET 2 A 5 HIS A 96 ILE A 101 1 N LEU A 97 O THR A 131 SHEET 3 A 5 ILE A 142 ALA A 147 1 O ILE A 144 N ARG A 100 SHEET 4 A 5 ALA A 178 ASP A 181 1 O PHE A 180 N ALA A 147 SHEET 5 A 5 ALA A 165 ALA A 167 -1 N HIS A 166 O HIS A 179 SHEET 1 B 2 TRP A 186 THR A 187 0 SHEET 2 B 2 THR A 193 ASN A 194 1 O THR A 193 N THR A 187 SHEET 1 C 5 THR B 131 ARG B 134 0 SHEET 2 C 5 HIS B 96 ILE B 101 1 N LEU B 97 O THR B 131 SHEET 3 C 5 ILE B 142 ALA B 147 1 O ILE B 144 N ARG B 100 SHEET 4 C 5 ALA B 178 ASP B 181 1 O PHE B 180 N ALA B 147 SHEET 5 C 5 ALA B 165 ALA B 167 -1 N HIS B 166 O HIS B 179 SHEET 1 D 2 TRP B 186 THR B 187 0 SHEET 2 D 2 THR B 193 ASN B 194 1 O THR B 193 N THR B 187 LINK OD2 ASP A 107 CA CA A 305 1555 1555 2.39 LINK OD1 ASP A 107 CA CA A 305 1555 1555 2.58 LINK O ASP A 141 CA CA A 304 1555 1555 2.33 LINK NE2 HIS A 151 ZN ZN A 302 1555 1555 2.00 LINK OD2 ASP A 153 ZN ZN A 302 1555 1555 2.26 LINK OD1 ASP A 158 CA CA A 303 1555 1555 2.31 LINK O GLY A 159 CA CA A 303 1555 1555 2.34 LINK O GLY A 161 CA CA A 303 1555 1555 2.34 LINK O VAL A 163 CA CA A 303 1555 1555 2.28 LINK NE2 HIS A 166 ZN ZN A 302 1555 1555 1.98 LINK O GLY A 173 CA CA A 304 1555 1555 2.31 LINK O ASN A 175 CA CA A 304 1555 1555 2.32 LINK OD1 ASP A 177 CA CA A 304 1555 1555 2.40 LINK ND1 HIS A 179 ZN ZN A 302 1555 1555 2.03 LINK OD2 ASP A 181 CA CA A 303 1555 1555 2.33 LINK O ASP A 182 CA CA A 305 1555 1555 2.34 LINK OD1 ASP A 182 CA CA A 305 1555 1555 2.48 LINK OE2 GLU A 184 CA CA A 303 1555 1555 2.22 LINK O GLU A 184 CA CA A 305 1555 1555 2.43 LINK NE2 HIS A 201 ZN ZN A 301 1555 1555 1.92 LINK NE2 HIS A 205 ZN ZN A 301 1555 1555 2.05 LINK NE2 HIS A 211 ZN ZN A 301 1555 1555 2.07 LINK CA CA A 304 O HOH A 401 1555 1555 2.32 LINK CA CA A 304 O HOH A 443 1555 1555 2.32 LINK CA CA A 305 O HOH A 405 1555 1555 2.30 LINK CA CA A 305 O HOH A 415 1555 1555 2.31 LINK OD2 ASP B 107 CA CA B 305 1555 1555 2.45 LINK OD1 ASP B 107 CA CA B 305 1555 1555 2.55 LINK OE1 GLU B 139 PT PT B 307 1555 1555 2.03 LINK O ASP B 141 CA CA B 304 1555 1555 2.36 LINK NE2 HIS B 151 ZN ZN B 302 1555 1555 2.14 LINK OD2 ASP B 153 ZN ZN B 302 1555 1555 2.00 LINK OD1 ASP B 158 CA CA B 303 1555 1555 2.25 LINK O GLY B 159 CA CA B 303 1555 1555 2.42 LINK O GLY B 161 CA CA B 303 1555 1555 2.44 LINK O VAL B 163 CA CA B 303 1555 1555 2.29 LINK NE2 HIS B 166 ZN ZN B 302 1555 1555 1.91 LINK O GLY B 173 CA CA B 304 1555 1555 2.37 LINK O ASN B 175 CA CA B 304 1555 1555 2.38 LINK OD1 ASP B 177 CA CA B 304 1555 1555 2.40 LINK ND1 HIS B 179 ZN ZN B 302 1555 1555 2.14 LINK OD2 ASP B 181 CA CA B 303 1555 1555 2.34 LINK O ASP B 182 CA CA B 305 1555 1555 2.34 LINK OD1 ASP B 182 CA CA B 305 1555 1555 2.43 LINK OE2 GLU B 184 CA CA B 303 1555 1555 2.30 LINK O GLU B 184 CA CA B 305 1555 1555 2.31 LINK NE2 HIS B 201 ZN ZN B 301 1555 1555 2.14 LINK NE2 HIS B 205 ZN ZN B 301 1555 1555 2.07 LINK NE2 HIS B 211 ZN ZN B 301 1555 1555 2.26 LINK ND1 HIS B 224 PT PT B 308 1555 1555 2.20 LINK ZN ZN B 301 O5 NGH B 306 1555 1555 2.18 LINK ZN ZN B 301 O4 NGH B 306 1555 1555 2.33 LINK CA CA B 304 O HOH B 402 1555 1555 2.34 LINK CA CA B 304 O HOH B 404 1555 1555 2.18 LINK CA CA B 305 O HOH B 444 1555 1555 2.45 LINK CA CA B 305 O HOH B 454 1555 1555 2.47 LINK PT PT B 307 O HOH B 440 1555 1555 1.99 LINK PT PT B 308 O HOH B 420 1555 1555 2.24 CISPEP 1 LEU A 226 THR A 227 0 0.44 CISPEP 2 THR B 227 ASP B 228 0 7.86 SITE 1 AC1 4 HIS A 201 HIS A 205 HIS A 211 THR B 255 SITE 1 AC2 4 HIS A 151 ASP A 153 HIS A 166 HIS A 179 SITE 1 AC3 6 ASP A 158 GLY A 159 GLY A 161 VAL A 163 SITE 2 AC3 6 ASP A 181 GLU A 184 SITE 1 AC4 6 ASP A 141 GLY A 173 ASN A 175 ASP A 177 SITE 2 AC4 6 HOH A 401 HOH A 443 SITE 1 AC5 5 ASP A 107 ASP A 182 GLU A 184 HOH A 405 SITE 2 AC5 5 HOH A 415 SITE 1 AC6 4 GLU A 139 MET A 143 CL A 307 HOH A 444 SITE 1 AC7 3 ALA A 140 MET A 143 PT A 306 SITE 1 AC8 4 HIS B 201 HIS B 205 HIS B 211 NGH B 306 SITE 1 AC9 4 HIS B 151 ASP B 153 HIS B 166 HIS B 179 SITE 1 BC1 6 ASP B 158 GLY B 159 GLY B 161 VAL B 163 SITE 2 BC1 6 ASP B 181 GLU B 184 SITE 1 BC2 6 ASP B 141 GLY B 173 ASN B 175 ASP B 177 SITE 2 BC2 6 HOH B 402 HOH B 404 SITE 1 BC3 5 ASP B 107 ASP B 182 GLU B 184 HOH B 444 SITE 2 BC3 5 HOH B 454 SITE 1 BC4 12 ASN B 162 VAL B 163 LEU B 164 ALA B 165 SITE 2 BC4 12 HIS B 201 GLU B 202 HIS B 205 HIS B 211 SITE 3 BC4 12 PRO B 221 TYR B 223 ZN B 301 HOH B 437 SITE 1 BC5 4 GLU B 139 MET B 143 CL B 309 HOH B 440 SITE 1 BC6 4 HIS B 224 CL B 310 CL B 311 HOH B 420 SITE 1 BC7 2 MET B 143 PT B 307 SITE 1 BC8 5 TYR B 223 HIS B 224 PT B 308 CL B 311 SITE 2 BC8 5 HOH B 420 SITE 1 BC9 5 GLY A 88 HIS B 224 PT B 308 CL B 310 SITE 2 BC9 5 HOH B 420 CRYST1 38.119 77.615 106.048 90.00 90.00 90.00 P 21 21 21 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 0.026234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009430 0.00000