Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTATED CATALYTIC DOMAIN OF HUMAN MMP12 IN COMPLEX WITH AN HYDROXAMATE ANALOGUE OF RXP470
 
Authors :  C. Rouanet-Mehouas, L. Devel, V. Dive, E. A. Stura
Date :  05 Aug 15  (Deposition) - 17 Aug 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Metzincin, Matrix Metallo Elastase, Mmp12, Human, Rxp470, Macrophage, Hydrolase, Hydroxamate Based Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Rouanet-Mehouas, B. Czarny, F. Beau, E. Cassar-Lajeunesse, E. A. Stura, V. Dive, L. Devel
Zinc-Metalloproteinase Inhibitors: Evaluation Of The Comple Role Played By The Zinc-Binding Group On Potency And Selectivity.
J. Med. Chem. V. 60 403 2017
PubMed-ID: 27996256  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01420

(-) Compounds

Molecule 1 - MACROPHAGE METALLOELASTASE
    Chains: A
    EC Number: 3.4.24.65
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET24A
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN UNP RESIDUES 106-263
    Gene: MMP12, HME
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- 12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
156O1Ligand/IonN-[(2R)-2-{[3-(3'-CHLOROBIPHENYL-4-YL)-1,2-OXAZOL-5-YL]METHYL}-4-(HYDROXYAMINO)-4-OXOBUTANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMINE
2CA3Ligand/IonCALCIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , 56O A:306binding site for residue ZN A 301
2AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196binding site for residue ZN A 302
3AC3SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:441 , HOH A:456binding site for residue CA A 303
4AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:552 , HOH A:588binding site for residue CA A 304
5AC5SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201binding site for residue CA A 305
6AC6SOFTWARETHR A:154 , GLY A:155 , GLY A:178 , GLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , THR A:215 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , PRO A:232 , LYS A:233 , ALA A:234 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , LYS A:241 , VAL A:243 , PHE A:248 , ZN A:301 , HOH A:401 , HOH A:404 , HOH A:406 , HOH A:407 , HOH A:411 , HOH A:416 , HOH A:422 , HOH A:424 , HOH A:578binding site for residue 56O A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D2B)

(-) Exons   (0, 0)

(no "Exon" information available for 5D2B)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d2b A 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5D2B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D2B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D2B)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    56O  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5d2b)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5d2b
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MMP12_HUMAN | P39900
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.65
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MMP12_HUMAN | P39900
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MMP12_HUMAN | P39900: 1jiz 1jk3 1os2 1os9 1rmz 1ros 1utt 1utz 1y93 1ycm 1z3j 2hu6 2jxy 2k2g 2k9c 2krj 2mlr 2mls 2n8r 2oxu 2oxw 2oxz 2poj 2w0d 2wo8 2wo9 2woa 2z2d 3ba0 3ehx 3ehy 3f15 3f16 3f17 3f18 3f19 3f1a 3lik 3lil 3lir 3ljg 3lk8 3lka 3n2u 3n2v 3nx7 3rts 3rtt 3ts4 3tsk 3uvc 4efs 4gql 4gr0 4gr3 4gr8 4guy 4h30 4h49 4h76 4h84 4i03 4ijo 5cxa 5czm 5d3c 5i0l 5i2z 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D2B)