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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A TWIN INHIBITOR.
 
Authors :  C. Antoni, E. A. Stura, L. Vera, E. Nuti, L. Carafa, E. Cassar-Lajeuness A. Rossello
Date :  13 Sep 12  (Deposition) - 24 Apr 13  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Divalent Inhibitor, Carboxylic Twin Inhibitor, Dimerisation, Metzincin, Zinc Protease, Hydrolase-Hydrolase Inhibtior Complex, 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

(-) Compounds

Molecule 1 - MACROPHAGE METALLOELASTASE
    Chains: A, B
    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: HUMAN MMP12 CATALYTIC DOMAIN (UNP RESIDUES 106-263)
    Gene: HME, MMP12
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MME, MACROPHAGE ELASTASE, ME, HME, MATRIX METALLOPROTEINASE- 12, MMP-12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
10ZD1Ligand/IonN,N'-BIS(2-[(BIPHENYL-4YLSULFONYL)[(2R)-1-HYDROXY-3-METHYL-1-OXOBUTAN-2-YL]-AMINO]ETHYL)BENZENE-1,3-DICARBOXAMIDE
2CA6Ligand/IonCALCIUM ION
3GOL8Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZN4Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , 0ZD B: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:416 , HOH A:424BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:404 , HOH A:405BINDING 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
06AC6SOFTWAREVAL A:144 , THR A:145 , PRO A:146 , LYS A:151 , ASN A:153 , GLN A:259 , HOH A:437 , HOH A:498 , HOH A:538BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREASP A:170 , HIS A:172 , PHE A:185 , ILE A:191 , SER B:207 , GLY B:208BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWARETYR A:132 , LYS A:136 , PHE A:213 , ILE A:245 , HOH A:532BINDING SITE FOR RESIDUE GOL A 308
09AC9SOFTWAREVAL A:108 , TRP A:109 , ARG A:110 , GLY A:188 , SER A:189 , HOH A:490 , HOH A:536BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREPRO A:232 , ALA A:234 , VAL A:235 , LYS A:241 , VAL A:243 , HOH A:501 , HOH A:503 , HOH A:568BINDING SITE FOR RESIDUE GOL A 310
11BC2SOFTWAREHIS A:172 , ALA A:184 , PHE A:185 , HOH A:435BINDING SITE FOR RESIDUE GOL A 311
12BC3SOFTWAREHIS B:218 , HIS B:222 , HIS B:228 , 0ZD B:306BINDING SITE FOR RESIDUE ZN B 301
13BC4SOFTWAREHIS B:168 , ASP B:170 , HIS B:183 , HIS B:196BINDING SITE FOR RESIDUE ZN B 302
14BC5SOFTWAREARG A:110 , ASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:442BINDING SITE FOR RESIDUE CA B 303
15BC6SOFTWAREASP B:124 , GLU B:199 , GLU B:201 , HOH B:407 , HOH B:408BINDING SITE FOR RESIDUE CA B 304
16BC7SOFTWAREASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201BINDING SITE FOR RESIDUE CA B 305
17BC8SOFTWAREILE A:180 , LEU A:181 , ALA A:182 , LEU A:214 , THR A:215 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , ZN A:301 , HOH A:401 , HOH A:433 , ILE B:180 , LEU B:181 , ALA B:182 , LEU B:214 , THR B:215 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , VAL B:235 , PHE B:237 , PRO B:238 , THR B:239 , TYR B:240 , ZN B:301 , GOL B:308 , HOH B:438 , HOH B:449 , HOH B:451 , HOH B:472 , HOH B:514BINDING SITE FOR RESIDUE 0ZD B 306
18BC9SOFTWAREMET B:105 , GLY B:225 , LEU B:226 , GLY B:227 , GLY B:257 , SER B:260 , LEU B:261 , HOH B:532BINDING SITE FOR RESIDUE GOL B 307
19CC1SOFTWARESER B:229 , SER B:230 , PRO B:238 , 0ZD B:306BINDING SITE FOR RESIDUE GOL B 308
20CC2SOFTWAREASP B:171 , HIS B:172 , HOH B:467 , HOH B:468 , HOH B:550 , HOH B:585 , HOH B:610BINDING SITE FOR RESIDUE PEG B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H30)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:106 -Pro B:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H30)

(-) Exons   (0, 0)

(no "Exon" information available for 4H30)

(-) 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 d4h30a_ A: automated matches                                                                                                                                    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
                 4h30 A 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         


Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains d4h30b_ B: 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
                 4h30 B 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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H30)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:106 - Pro B:107   [ 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 | 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 4h49 4h76 4h84 4i03 4ijo 5cxa 5czm 5d2b 5d3c 5i0l 5i2z 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

3lir HUMAN MMP12 IN COMPLEX WITH NON-ZINC CHELATING INHIBITOR.
4efs HUMAN MMP12 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR.
4h1q CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
4h2e CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR
4h3x