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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MMP12 IN COMPLEX WITH SELECTIVE PHOSPHINIC INHIBITOR RXP470.1
 
Authors :  E. A. Stura, L. Vera, F. Beau, L. Devel, E. Cassar-Lajeunesse, V. Dive
Date :  23 Aug 12  (Deposition) - 06 Feb 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Potent Selective Phosphinic Inhibitor, Metzincin, Zinc Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Czarny, E. A. Stura, L. Devel, L. Vera, E. Cassar-Lajeunesse, F. Beau, V. Calderone, M. Fragai, C. Luchinat, V. Dive
Molecular Determinants Of A Selective Matrix Metalloprotease-12 Inhibitor: Insights From Crystallography And Thermodynamic Studies.
J. Med. Chem. V. 56 1149 2013
PubMed-ID: 23343195  |  Reference-DOI: 10.1021/JM301574D

(-) Compounds

Molecule 1 - MACROPHAGE METALLOELASTASE
    ChainsA
    EC Number3.4.24.65
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN (UNP RESIDUES 106-263)
    GeneHME, MMP12
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMME, 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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2R471Ligand/IonN-[(2S)-3-[(S)-(4-BROMOPHENYL)(HYDROXY)PHOSPHORYL]-2-{[3-(3'-CHLOROBIPHENYL-4-YL)-1,2-OXAZOL-5-YL]METHYL}PROPANOYL]-L-ALPHA-GLUTAMYL-L-ALPHA-GLUTAMINE
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , R47 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:417 , HOH A:423 , HOH A:648BINDING SITE FOR RESIDUE CA A 303
4AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:424 , HOH A:436BINDING 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 , HIS A:172 , GLY A:178 , GLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:183 , 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 , THR A:239 , TYR A:240 , LYS A:241 , VAL A:243 , PHE A:248 , ZN A:301 , HOH A:401 , HOH A:421 , HOH A:462 , HOH A:469 , HOH A:479 , HOH A:489 , HOH A:501 , HOH A:504 , HOH A:505 , HOH A:573 , HOH A:581 , HOH A:609 , HOH A:618 , HOH A:630 , HOH A:667 , HOH A:703BINDING SITE FOR RESIDUE R47 A 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:105 -Gly A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GQL)

(-) 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 d4gqla_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gql 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)
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  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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Met A:105 - Gly A:106   [ RasMol ]  
 

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  MMP12_HUMAN | P39900
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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP12_HUMAN | P399001jiz 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 4gr0 4gr3 4gr8 4guy 4h30 4h49 4h76 4h84 4i03 4ijo 5cxa 5czm 5d2b 5d3c 5i0l 5i2z 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

3lik HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR
3lil HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR
3lir HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR
3ljg HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR
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
4gr0
4gr3
4gr8