10 20 30 40 50 60 70 80 4I03 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/HYDROLASE INHIBITOR 16-NOV-12 4I03
TITLE HUMAN MMP12 IN COMPLEX WITH A PEG-LINKED BIFUNCTIONAL L-GLUTAMATE TITLE 2 MOTIF INHIBITOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 106-263); COMPND 5 SYNONYM: MME, MACROPHAGE ELASTASE, ME, HME, MATRIX METALLOPROTEINASE- COMPND 6 12, MMP-12; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: ESCHERICHIA COLI; SOURCE 6 GENE: HME, MMP12; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET24A
KEYWDS SELECTIVE CARBOXYLATE BASED MMP-12 BIFUNCTIONAL INHIBITOR, METZINCIN, KEYWDS 2 ZINC PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR E.A.STURA,L.VERA,L.DEVEL,E.CASSAR-LAJEUNESSE,V.DIVE
REVDAT 2 03-JUL-13 4I03 1 JRNL REVDAT 1 24-APR-13 4I03 0
JRNL AUTH C.ANTONI,L.VERA,L.DEVEL,M.P.CATALANI,B.CZARNY, JRNL AUTH 2 E.CASSAR-LAJEUNESSE,E.NUTI,A.ROSSELLO,V.DIVE,E.A.STURA JRNL TITL CRYSTALLIZATION OF BI-FUNCTIONAL LIGAND PROTEIN COMPLEXES. JRNL REF J.STRUCT.BIOL. V. 182 246 2013 JRNL REFN ISSN 1047-8477 JRNL PMID 23567804 JRNL DOI 10.1016/J.JSB.2013.03.015
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.ROSSELLO,E.NUTI,M.P.CATALANI,P.CARELLI,E.ORLANDINI, REMARK 1 AUTH 2 S.RAPPOSELLI,T.TUCCINARDI,S.J.ATKINSON,G.MURPHY,A.BALSAMO REMARK 1 TITL A NEW DEVELOPMENT OF MATRIX METALLOPROTEINASE INHIBITORS: REMARK 1 TITL 2 TWIN HYDROXAMIC ACIDS AS POTENT INHIBITORS OF MMPS. REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 15 2311 2005 REMARK 1 REFN ISSN 0960-894X REMARK 1 PMID 15837315 REMARK 1 DOI 10.1016/J.BMCL.2005.03.002 REMARK 1 REFERENCE 2 REMARK 1 REFN ISSN 0960-894X
REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15828 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 : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 834 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1124 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 139 REMARK 3 SOLVENT ATOMS : 171 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.294 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1501 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1045 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2015 ; 2.038 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2515 ; 1.033 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 176 ; 7.055 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 66 ;35.842 ;22.879 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 215 ;16.634 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.651 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 197 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1673 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 343 ; 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): 836 ; 1.372 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 347 ; 0.414 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1349 ; 2.290 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 665 ; 3.131 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 664 ; 4.865 ; 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 : 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 4I03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-12. REMARK 100 THE RCSB ID CODE IS RCSB076135.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980110 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16663 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.140 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : 0.08900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.02 REMARK 200 R MERGE FOR SHELL (I) : 0.88700 REMARK 200 R SYM FOR SHELL (I) : 0.76800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.710 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: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 222 MICROM MMP12 REMARK 280 MUTANT E219A 106 MICROM BIFUNCTIONAL INHIBITOR LD884. RESERVOIR: REMARK 280 27% PEG 10K, 150MM IMIDAZOLE PIPERIDINE, PH 8.5. CRYOPROTECTANT: REMARK 280 5 % DI-ETHYLENE GLYCOL + 5 % ETHYLENE GLYCOL + 10 % 1,2- REMARK 280 PROPANEDIOL + 5 % DMSO + 5 % GLYCEROL, 25% MPEG 5K, 100MM (NA REMARK 280 ACETATE, ADA, BICINE 10% PH 4.0/90% PH 9.0), VAPOR DIFFUSION, REMARK 280 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 25.89500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.89500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.05000 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 300 REMARK: THE BIFUNCTIONAL INHIBITOR JOINS TWO MMP-12 MOLECULES REMARK 300 CREATING A CRYSTALLOGRAPHIC DIMER
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 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 484 LIES ON A SPECIAL POSITION.
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 110 42.92 -106.67 REMARK 500 HIS A 206 -155.45 -134.43 REMARK 500 THR A 247 1.07 91.30 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 ASP A 170 OD2 REMARK 620 2 HIS A 196 ND1 93.3 REMARK 620 3 HIS A 168 NE2 108.2 106.3 REMARK 620 N 1 2 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 228 NE2 105.1 REMARK 620 3 L88 A 306 O4 131.4 91.8 REMARK 620 4 L88 A 306 O4E 87.4 136.5 52.4 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 GLY A 192 O REMARK 620 2 ASP A 158 O 92.5 REMARK 620 3 HOH A 414 O 170.7 90.9 REMARK 620 4 GLY A 190 O 89.0 166.0 85.6 REMARK 620 5 HOH A 419 O 83.0 84.1 88.7 82.3 REMARK 620 6 ASP A 194 OD1 92.2 91.4 96.4 102.4 173.3 REMARK 620 N 1 2 3 4 5 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 198 OD2 REMARK 620 2 ASP A 175 OD1 93.9 REMARK 620 3 GLU A 201 OE2 94.9 168.7 REMARK 620 4 ILE A 180 O 91.0 97.8 89.3 REMARK 620 5 GLY A 176 O 89.8 85.2 87.6 176.9 REMARK 620 6 GLY A 178 O 172.4 85.0 85.4 96.7 82.6 REMARK 620 N 1 2 3 4 5 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 OD2 REMARK 620 2 GLU A 199 O 138.4 REMARK 620 3 GLU A 199 OE2 86.7 80.7 REMARK 620 4 GLU A 201 O 74.8 75.0 114.6 REMARK 620 5 HOH A 420 O 98.0 102.8 167.6 77.7 REMARK 620 6 HOH A 429 O 136.7 82.6 88.4 144.1 80.3 REMARK 620 7 ASP A 124 OD1 52.8 162.3 87.4 122.2 86.3 84.0 REMARK 620 N 1 2 3 4 5 6
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 L88 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGO A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 318
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EFS RELATED DB: PDB REMARK 900 HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR REMARK 900 RELATED ID: 3TS4 RELATED DB: PDB REMARK 900 HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR REMARK 900 RELATED ID: 3TSK RELATED DB: PDB REMARK 900 HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR REMARK 900 RELATED ID: 4H30 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN REMARK 900 COMPLEX WITH A TWIN INHIBITOR. REMARK 900 RELATED ID: 4H49 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CRYSTAL STRUCTURE OF THE CATALYTIC REMARK 900 DOMAIN OF MMP-12 IN COMPLEX WITH A TWIN INHIBITOR.
DBREF 4I03 A 106 263 UNP P39900 MMP12_HUMAN 106 263
SEQADV 4I03 MET A 105 UNP P39900 INITIATING METHIONINE SEQADV 4I03 ASP A 171 UNP P39900 PHE 171 ENGINEERED MUTATION SEQADV 4I03 ALA A 219 UNP P39900 GLU 219 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 ALA 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 L88 A 306 75 HET GOL A 307 6 HET GOL A 308 12 HET GOL A 309 6 HET PGO A 310 5 HET PGO A 311 5 HET DMS A 312 4 HET DMS A 313 4 HET EDO A 314 4 HET EDO A 315 4 HET EDO A 316 4 HET EDO A 317 4 HET PEG A 318 7
HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM L88 (4R,22R)-5,21-DIOXO-4,22-BIS({3-[4-(4-PHENYLTHIOPHEN-2- HETNAM 2 L88 YL)PHENYL]PROPANOYL}AMINO)-10,13,16-TRIOXA-6,20- HETNAM 3 L88 DIAZAPENTACOSANE-1,25-DIOIC ACID HETNAM GOL GLYCEROL HETNAM PGO S-1,2-PROPANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA 3(CA 2+) FORMUL 7 L88 C58 H66 N4 O11 S2 FORMUL 8 GOL 3(C3 H8 O3) FORMUL 11 PGO 2(C3 H8 O2) FORMUL 13 DMS 2(C2 H6 O S) FORMUL 15 EDO 4(C2 H6 O2) FORMUL 19 PEG C4 H10 O3 FORMUL 20 HOH *171(H2 O)
HELIX 1 1 ASN A 126 ASN A 143 1 18 HELIX 2 2 LEU A 212 LEU A 224 1 13 HELIX 3 3 SER A 251 GLY A 263 1 13
SHEET 1 A 5 LYS A 148 LYS A 151 0 SHEET 2 A 5 TYR A 113 ILE A 118 1 N ILE A 114 O LYS A 148 SHEET 3 A 5 ILE A 159 ALA A 164 1 O VAL A 161 N ARG A 117 SHEET 4 A 5 ALA A 195 ASP A 198 1 O PHE A 197 N VAL A 162 SHEET 5 A 5 ALA A 182 ALA A 184 -1 N HIS A 183 O HIS A 196 SHEET 1 B 2 TRP A 203 THR A 204 0 SHEET 2 B 2 THR A 210 ASN A 211 1 O THR A 210 N THR A 204
LINK OD2 ASP A 170 ZN ZN A 302 1555 1555 1.88 LINK ND1 HIS A 196 ZN ZN A 302 1555 1555 2.01 LINK NE2 HIS A 168 ZN ZN A 302 1555 1555 2.06 LINK NE2 HIS A 222 ZN ZN A 301 1555 1555 2.06 LINK NE2 HIS A 228 ZN ZN A 301 1555 1555 2.11 LINK O GLY A 192 CA CA A 303 1555 1555 2.16 LINK O ASP A 158 CA CA A 303 1555 1555 2.24 LINK OD2 ASP A 198 CA CA A 305 1555 1555 2.27 LINK OD1 ASP A 175 CA CA A 305 1555 1555 2.29 LINK OE2 GLU A 201 CA CA A 305 1555 1555 2.30 LINK CA CA A 303 O HOH A 414 1555 1555 2.31 LINK OD2 ASP A 124 CA CA A 304 1555 1555 2.31 LINK O ILE A 180 CA CA A 305 1555 1555 2.31 LINK O GLU A 199 CA CA A 304 1555 1555 2.33 LINK O GLY A 176 CA CA A 305 1555 1555 2.36 LINK O GLY A 178 CA CA A 305 1555 1555 2.36 LINK OE2 GLU A 199 CA CA A 304 1555 1555 2.37 LINK ZN ZN A 301 O4 L88 A 306 1555 1555 2.39 LINK O GLY A 190 CA CA A 303 1555 1555 2.39 LINK ZN ZN A 301 O4E L88 A 306 1555 1555 2.44 LINK CA CA A 303 O HOH A 419 1555 1555 2.45 LINK O GLU A 201 CA CA A 304 1555 1555 2.46 LINK CA CA A 304 O HOH A 420 1555 1555 2.48 LINK CA CA A 304 O HOH A 429 1555 1555 2.50 LINK OD1 ASP A 194 CA CA A 303 1555 1555 2.50 LINK OD1 ASP A 124 CA CA A 304 1555 1555 2.56
SITE 1 AC1 4 HIS A 218 HIS A 222 HIS A 228 L88 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 419 SITE 1 AC4 5 ASP A 124 GLU A 199 GLU A 201 HOH A 420 SITE 2 AC4 5 HOH A 429 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 218 HIS A 222 HIS A 228 PRO A 232 SITE 3 AC6 21 LYS A 233 ALA A 234 VAL A 235 PHE A 237 SITE 4 AC6 21 PRO A 238 THR A 239 TYR A 240 LYS A 241 SITE 5 AC6 21 ZN A 301 PGO A 311 HOH A 401 HOH A 513 SITE 6 AC6 21 HOH A 521 SITE 1 AC7 11 TYR A 113 THR A 115 MET A 125 ASN A 126 SITE 2 AC7 11 ASP A 129 SER A 150 THR A 204 THR A 205 SITE 3 AC7 11 HOH A 435 HOH A 454 HOH A 468 SITE 1 AC8 9 MET A 105 GLY A 106 VAL A 108 ARG A 110 SITE 2 AC8 9 GLY A 176 LYS A 177 SER A 260 LEU A 261 SITE 3 AC8 9 EDO A 315 SITE 1 AC9 8 MET A 105 ASP A 171 GLY A 225 LEU A 226 SITE 2 AC9 8 GLY A 227 SER A 260 LEU A 261 HOH A 428 SITE 1 BC1 1 ARG A 256 SITE 1 BC2 5 GLY A 179 THR A 239 TYR A 240 L88 A 306 SITE 2 BC2 5 HOH A 500 SITE 1 BC3 4 HIS A 172 HIS A 183 ALA A 184 EDO A 316 SITE 1 BC4 7 ASP A 175 LYS A 177 GLY A 178 GLY A 179 SITE 2 BC4 7 THR A 239 LYS A 241 EDO A 315 SITE 1 BC5 4 ARG A 110 ASP A 200 EDO A 315 HOH A 505 SITE 1 BC6 6 MET A 105 ASP A 175 PHE A 237 GOL A 308 SITE 2 BC6 6 DMS A 313 EDO A 314 SITE 1 BC7 5 ALA A 184 DMS A 312 HOH A 401 HOH A 421 SITE 2 BC7 5 HOH A 503 SITE 1 BC8 3 HIS A 168 HIS A 196 HOH A 405 SITE 1 BC9 8 THR A 145 PRO A 146 SER A 150 PHE A 202 SITE 2 BC9 8 HIS A 206 HOH A 454 HOH A 519 HOH A 520
CRYST1 51.790 60.100 54.920 90.00 116.67 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 0.019309 0.000000 0.009699 0.00000
SCALE2 0.000000 0.016639 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020376 0.00000