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 :  HUMAN MMP12 IN COMPLEX WITH A PEG-LINKED BIFUNCTIONAL L-GLUTAMATE MOTIF INHIBITOR
 
Authors :  E. A. Stura, L. Vera, L. Devel, E. Cassar-Lajeunesse, V. Dive
Date :  16 Nov 12  (Deposition) - 24 Apr 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Selective Carboxylate Based Mmp-12 Bifunctional Inhibitor, Metzincin, Zinc Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Antoni, L. Vera, L. Devel, M. P. Catalani, B. Czarny, E. Cassar-Lajeunesse, E. Nuti, A. Rossello, V. Dive, E. A. Stura
Crystallization Of Bi-Functional Ligand Protein Complexes.
J. Struct. Biol. V. 182 246 2013
PubMed-ID: 23567804  |  Reference-DOI: 10.1016/J.JSB.2013.03.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MACROPHAGE METALLOELASTASE
    Chains: A
    EC Number: 3.4.24.65
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 106-263)
    Gene: HME, MMP12
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: ESCHERICHIA COLI
    Synonym: MME, MACROPHAGE ELASTASE, ME, 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  (8, 18)

Asymmetric/Biological Unit (8, 18)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3EDO4Ligand/Ion1,2-ETHANEDIOL
4GOL3Ligand/IonGLYCEROL
5L881Ligand/Ion(4R,22R)-5,21-DIOXO-4,22-BIS({3-[4-(4-PHENYLTHIOPHEN-2-YL)PHENYL]PROPANOYL}AMINO)-10,13,16-TRIOXA-6,20-DIAZAPENTACOSANE-1,25-DIOIC ACID
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7PGO2Ligand/IonS-1,2-PROPANEDIOL
8ZN2Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , L88 A:306BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:414 , HOH A:419BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:420 , HOH A:429BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWAREGLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:218 , 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 , ZN A:301 , PGO A:311 , HOH A:401 , HOH A:513 , HOH A:521BINDING SITE FOR RESIDUE L88 A 306
07AC7SOFTWARETYR A:113 , THR A:115 , MET A:125 , ASN A:126 , ASP A:129 , SER A:150 , THR A:204 , THR A:205 , HOH A:435 , HOH A:454 , HOH A:468BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWAREMET A:105 , GLY A:106 , VAL A:108 , ARG A:110 , GLY A:176 , LYS A:177 , SER A:260 , LEU A:261 , EDO A:315BINDING SITE FOR RESIDUE GOL A 308
09AC9SOFTWAREMET A:105 , ASP A:171 , GLY A:225 , LEU A:226 , GLY A:227 , SER A:260 , LEU A:261 , HOH A:428BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREARG A:256BINDING SITE FOR RESIDUE PGO A 310
11BC2SOFTWAREGLY A:179 , THR A:239 , TYR A:240 , L88 A:306 , HOH A:500BINDING SITE FOR RESIDUE PGO A 311
12BC3SOFTWAREHIS A:172 , HIS A:183 , ALA A:184 , EDO A:316BINDING SITE FOR RESIDUE DMS A 312
13BC4SOFTWAREASP A:175 , LYS A:177 , GLY A:178 , GLY A:179 , THR A:239 , LYS A:241 , EDO A:315BINDING SITE FOR RESIDUE DMS A 313
14BC5SOFTWAREARG A:110 , ASP A:200 , EDO A:315 , HOH A:505BINDING SITE FOR RESIDUE EDO A 314
15BC6SOFTWAREMET A:105 , ASP A:175 , PHE A:237 , GOL A:308 , DMS A:313 , EDO A:314BINDING SITE FOR RESIDUE EDO A 315
16BC7SOFTWAREALA A:184 , DMS A:312 , HOH A:401 , HOH A:421 , HOH A:503BINDING SITE FOR RESIDUE EDO A 316
17BC8SOFTWAREHIS A:168 , HIS A:196 , HOH A:405BINDING SITE FOR RESIDUE EDO A 317
18BC9SOFTWARETHR A:145 , PRO A:146 , SER A:150 , PHE A:202 , HIS A:206 , HOH A:454 , HOH A:519 , HOH A:520BINDING SITE FOR RESIDUE PEG A 318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I03)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I03)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I03)

(-) Exons   (0, 0)

(no "Exon" information available for 4I03)

(-) 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 d4i03a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i03 A 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHAIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I03)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I03)

(-) 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    L88  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGO  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4i03)
 

(-) 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
  4i03
    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 4ijo 5cxa 5czm 5d2b 5d3c 5i0l 5i2z 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

3ts4 HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR
3tsk HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR
4efs HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR
4h30 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TWIN INHIBITOR.
4h49 CRYSTAL STRUCTURE OF CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TWIN INHIBITOR.