HEADER HYDROLASE 26-SEP-17 6EKN TITLE CRYSTAL STRUCTURE OF MMP12 IN COMPLEX WITH INHIBITOR BE7. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- COMPND 5 12; COMPND 6 EC: 3.4.24.65; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: METALLOPROTEASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: MACROPHAGE; SOURCE 6 GENE: MMP12, HME; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METZINCIN, CARBOXYLATE INHIBITOR ALTERNATIVE ZINC-BINDING GROUPS, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.CICCONE,L.TEPSHI,E.NUTI,A.ROSSELLO,E.A.STURA REVDAT 3 17-JAN-24 6EKN 1 LINK REVDAT 2 06-JUN-18 6EKN 1 JRNL REVDAT 1 16-MAY-18 6EKN 0 JRNL AUTH E.NUTI,D.CUFFARO,E.BERNARDINI,C.CAMODECA,L.PANELLI,S.CHAVES, JRNL AUTH 2 L.CICCONE,L.TEPSHI,L.VERA,E.ORLANDINI,S.NENCETTI,E.A.STURA, JRNL AUTH 3 M.A.SANTOS,V.DIVE,A.ROSSELLO JRNL TITL DEVELOPMENT OF THIOARYL-BASED MATRIX METALLOPROTEINASE-12 JRNL TITL 2 INHIBITORS WITH ALTERNATIVE ZINC-BINDING GROUPS: SYNTHESIS, JRNL TITL 3 POTENTIOMETRIC, NMR, AND CRYSTALLOGRAPHIC STUDIES. JRNL REF J. MED. CHEM. V. 61 4421 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29727184 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00096 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 44626 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2349 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3104 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.6450 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.6360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.786 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1440 ; 0.027 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1263 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1965 ; 2.377 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2920 ; 1.180 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 181 ; 6.259 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;33.284 ;22.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 216 ;14.134 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.293 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 196 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1694 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 345 ; 0.003 ; 0.020 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): 697 ; 2.950 ; 1.745 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 696 ; 2.948 ; 1.740 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 887 ; 3.878 ; 2.612 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 888 ; 3.877 ; 2.613 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 742 ; 4.594 ; 2.079 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 742 ; 4.594 ; 2.079 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1078 ; 4.587 ; 2.961 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1723 ; 5.075 ;22.257 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1691 ; 4.875 ;21.734 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2699 ; 8.512 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 84 ;22.953 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2728 ;10.025 ; 5.000 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 : NULL 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 6EKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980035 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : MICROFOCUS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46976 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 36.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.610 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 10.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.18 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.65000 REMARK 200 FOR SHELL : 0.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4I03 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 1 MICRO-L MMP12 AT 290 MICRO REMARK 280 -M WITH 10 MILLI-M ACETOHYDROXAMATE + 0.1 MICRO-L BE6 FROM 10 REMARK 280 MILII-M IN 100% DMSO PRECIPITANT: 17% PEG 20K, 250 MILLI-M NACL, REMARK 280 100 MILII-M TRIS HCL, PH 10.0. CRYOPROTECTANT: 40% (25 % DI- REMARK 280 ETHYLENE GLYCOL + 25 % GLYCEROL + 25 % 1,2-PROPANEDIOL) 10 % PEG REMARK 280 10K, 200 MILLI-M NACL, 100 MILLI-M AAB (NA ACETATE,N-(2- REMARK 280 ACETAMIDO)IMINODIACETIC ACID (ADA), BICINE) 10% ACID/90% BASIC, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.78000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.78000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.17500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 408 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 504 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 520 LIES ON A SPECIAL POSITION. 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 GLU A 128 CD GLU A 128 OE1 0.069 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 ASP A 171 -0.16 77.11 REMARK 500 HIS A 206 -154.18 -137.17 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 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 124 OD1 REMARK 620 2 ASP A 124 OD2 51.3 REMARK 620 3 GLU A 199 O 162.1 138.9 REMARK 620 4 GLU A 199 OE2 87.6 85.5 79.8 REMARK 620 5 GLU A 201 O 121.9 77.1 75.4 116.0 REMARK 620 6 HOH A 507 O 87.5 100.8 101.9 166.9 76.8 REMARK 620 7 HOH A 515 O 84.8 135.9 82.1 88.5 142.5 79.0 REMARK 620 N 1 2 3 4 5 6 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 O REMARK 620 2 GLY A 190 O 167.3 REMARK 620 3 GLY A 192 O 93.4 91.5 REMARK 620 4 ASP A 194 OD1 89.0 102.5 91.4 REMARK 620 5 HOH A 414 O 89.6 84.3 173.4 94.5 REMARK 620 6 HOH A 448 O 83.7 85.5 81.7 169.6 92.8 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 168 NE2 REMARK 620 2 ASP A 170 OD2 108.0 REMARK 620 3 ASP A 170 OD2 109.6 1.7 REMARK 620 4 HIS A 183 NE2 116.3 115.5 114.8 REMARK 620 5 HIS A 196 ND1 109.6 95.3 94.2 110.2 REMARK 620 N 1 2 3 4 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 175 OD1 REMARK 620 2 GLY A 176 O 88.7 REMARK 620 3 GLY A 178 O 85.7 85.0 REMARK 620 4 ILE A 180 O 97.2 172.0 90.1 REMARK 620 5 ILE A 180 O 86.7 172.9 100.0 15.0 REMARK 620 6 ASP A 198 OD2 94.3 90.2 175.2 94.7 84.8 REMARK 620 7 GLU A 201 OE2 168.4 88.8 82.8 84.3 96.7 97.0 REMARK 620 N 1 2 3 4 5 6 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 218 NE2 REMARK 620 2 HIS A 222 NE2 101.6 REMARK 620 3 HIS A 228 NE2 113.2 104.2 REMARK 620 4 B9N A 306 O26 116.5 123.2 97.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B9N A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 DBREF 6EKN A 106 263 UNP P39900 MMP12_HUMAN 106 263 SEQADV 6EKN MET A 105 UNP P39900 INITIATING METHIONINE SEQADV 6EKN ASP A 171 UNP P39900 PHE 171 ENGINEERED MUTATION SEQRES 1 A 159 MET GLY PRO VAL TRP ARG LYS HIS TYR ILE THR TYR ARG SEQRES 2 A 159 ILE ASN ASN TYR THR PRO ASP MET ASN ARG GLU ASP VAL SEQRES 3 A 159 ASP TYR ALA ILE ARG LYS ALA PHE GLN VAL TRP SER ASN SEQRES 4 A 159 VAL THR PRO LEU LYS PHE SER LYS ILE ASN THR GLY MET SEQRES 5 A 159 ALA ASP ILE LEU VAL VAL PHE ALA ARG GLY ALA HIS GLY SEQRES 6 A 159 ASP ASP HIS ALA PHE ASP GLY LYS GLY GLY ILE LEU ALA SEQRES 7 A 159 HIS ALA PHE GLY PRO GLY SER GLY ILE GLY GLY ASP ALA SEQRES 8 A 159 HIS PHE ASP GLU ASP GLU PHE TRP THR THR HIS SER GLY SEQRES 9 A 159 GLY THR ASN LEU PHE LEU THR ALA VAL HIS GLU ILE GLY SEQRES 10 A 159 HIS SER LEU GLY LEU GLY HIS SER SER ASP PRO LYS ALA SEQRES 11 A 159 VAL MET PHE PRO THR TYR LYS TYR VAL ASP ILE ASN THR SEQRES 12 A 159 PHE ARG LEU SER ALA ASP ASP ILE ARG GLY ILE GLN SER SEQRES 13 A 159 LEU TYR GLY 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 B9N A 306 32 HET EDO A 307 4 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM B9N (2~{S})-2-[2-[4-(4-METHOXYPHENYL) HETNAM 2 B9N PHENYL]SULFONYLPHENYL]PENTANEDIOIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 3(CA 2+) FORMUL 7 B9N C24 H22 O7 S FORMUL 8 EDO C2 H6 O2 FORMUL 9 HOH *146(H2 O) HELIX 1 AA1 ASN A 126 ASN A 143 1 18 HELIX 2 AA2 LEU A 212 LEU A 224 1 13 HELIX 3 AA3 SER A 251 GLY A 263 1 13 SHEET 1 AA1 5 LYS A 148 LYS A 151 0 SHEET 2 AA1 5 TYR A 113 ILE A 118 1 N ILE A 114 O LYS A 148 SHEET 3 AA1 5 ILE A 159 ALA A 164 1 O VAL A 161 N ARG A 117 SHEET 4 AA1 5 ALA A 195 ASP A 198 1 O PHE A 197 N VAL A 162 SHEET 5 AA1 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 AA2 2 TRP A 203 THR A 204 0 SHEET 2 AA2 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204 LINK OD1 ASP A 124 CA CA A 304 1555 1555 2.61 LINK OD2 ASP A 124 CA CA A 304 1555 1555 2.41 LINK O ASP A 158 CA CA A 303 1555 1555 2.34 LINK NE2 HIS A 168 ZN ZN A 302 1555 1555 1.99 LINK OD2AASP A 170 ZN ZN A 302 1555 1555 2.00 LINK OD2BASP A 170 ZN ZN A 302 1555 1555 1.96 LINK OD1 ASP A 175 CA CA A 305 1555 1555 2.34 LINK O GLY A 176 CA CA A 305 1555 1555 2.26 LINK O GLY A 178 CA CA A 305 1555 1555 2.33 LINK O AILE A 180 CA CA A 305 1555 1555 2.34 LINK O BILE A 180 CA CA A 305 1555 1555 2.39 LINK NE2 HIS A 183 ZN ZN A 302 1555 1555 1.98 LINK O GLY A 190 CA CA A 303 1555 1555 2.31 LINK O GLY A 192 CA CA A 303 1555 1555 2.25 LINK OD1 ASP A 194 CA CA A 303 1555 1555 2.41 LINK ND1 HIS A 196 ZN ZN A 302 1555 1555 2.06 LINK OD2 ASP A 198 CA CA A 305 1555 1555 2.31 LINK O GLU A 199 CA CA A 304 1555 1555 2.33 LINK OE2 GLU A 199 CA CA A 304 1555 1555 2.41 LINK O GLU A 201 CA CA A 304 1555 1555 2.39 LINK OE2 GLU A 201 CA CA A 305 1555 1555 2.33 LINK NE2 HIS A 218 ZN ZN A 301 1555 1555 2.04 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.06 LINK NE2 HIS A 228 ZN ZN A 301 1555 1555 1.92 LINK ZN ZN A 301 O26 B9N A 306 1555 1555 2.01 LINK CA CA A 303 O HOH A 414 1555 1555 2.27 LINK CA CA A 303 O HOH A 448 1555 1555 2.43 LINK CA CA A 304 O HOH A 507 1555 1555 2.39 LINK CA CA A 304 O HOH A 515 1555 1555 2.36 SITE 1 AC1 4 HIS A 218 HIS A 222 HIS A 228 B9N A 306 SITE 1 AC2 4 HIS A 168 ASP A 170 HIS A 183 HIS A 196 SITE 1 AC3 6 ASP A 158 GLY A 190 GLY A 192 ASP A 194 SITE 2 AC3 6 HOH A 414 HOH A 448 SITE 1 AC4 5 ASP A 124 GLU A 199 GLU A 201 HOH A 507 SITE 2 AC4 5 HOH A 515 SITE 1 AC5 6 ASP A 175 GLY A 176 GLY A 178 ILE A 180 SITE 2 AC5 6 ASP A 198 GLU A 201 SITE 1 AC6 21 GLY A 179 ILE A 180 LEU A 181 ALA A 182 SITE 2 AC6 21 HIS A 183 LEU A 214 HIS A 218 GLU A 219 SITE 3 AC6 21 HIS A 222 HIS A 228 VAL A 235 PHE A 237 SITE 4 AC6 21 PRO A 238 THR A 239 TYR A 240 ZN A 301 SITE 5 AC6 21 HOH A 431 HOH A 447 HOH A 468 HOH A 503 SITE 6 AC6 21 HOH A 510 SITE 1 AC7 5 ASN A 119 ASN A 120 ARG A 127 HOH A 472 SITE 2 AC7 5 HOH A 512 CRYST1 51.560 60.350 54.560 90.00 116.10 90.00 C 1 2 1 4 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 0.019395 0.000000 0.009501 0.00000 SCALE2 0.000000 0.016570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020410 0.00000