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(-) Description

Title :  X-RAY STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-8 WITH THE INHIBITOR ML115
 
Authors :  G. Pochetti, R. Montanari, D. Capelli, P. Tortorella
Date :  10 Jun 14  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Pochetti, R. Montanari, D. Capelli, P. Tortorella
X-Ray Structure Of The Complex Of The Catalytic Domain Of Mmp-8 And A Bis-Phosphonate Inhibitor (Ml115)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NEUTROPHIL COLLAGENASE
    ChainsA
    EC Number3.4.24.34
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, UNP RESIDUES 100-262
    GeneMMP8, CLG1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMATRIX METALLOPROTEINASE-8, MMP-8, PMNL COLLAGENASE, PMNL- CL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3QZK1Ligand/Ion{[(BIPHENYL-4-YLSULFONYL)AMINO]METHANEDIYL}BIS(PHOSPHONIC ACID)
4ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:137 , GLY A:169 , GLY A:171 , ASP A:173 , HOH A:408 , HOH A:412BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREASP A:154 , GLY A:155 , ASN A:157 , ILE A:159 , ASP A:177 , GLU A:180BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREHIS A:147 , ASP A:149 , HIS A:162 , HIS A:175BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREHIS A:197 , HIS A:201 , HIS A:207 , QZK A:305BINDING SITE FOR RESIDUE ZN A 304
5AC5SOFTWAREILE A:159 , LEU A:160 , ALA A:161 , HIS A:162 , LEU A:193 , HIS A:197 , GLU A:198 , HIS A:201 , HIS A:207 , LEU A:214 , TYR A:216 , PRO A:217 , ASN A:218 , TYR A:219 , ZN A:304 , HOH A:415 , HOH A:424 , HOH A:450 , HOH A:451 , HOH A:464 , HOH A:504 , HOH A:506 , HOH A:507BINDING SITE FOR RESIDUE QZK A 305
6AC6SOFTWAREASP A:115 , SER A:186 , PHE A:192 , THR A:224 , SER A:225 , TYR A:227 , HOH A:428 , HOH A:478 , HOH A:533BINDING SITE FOR RESIDUE MES A 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:188 -Tyr A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QKZ)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee............hhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qkz A  80 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239   

   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4QKZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:188 - Tyr A:189   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP8_HUMAN | P228941a85 1a86 1bzs 1i73 1i76 1jan 1jao 1jap 1jaq 1jh1 1jj9 1kbc 1mmb 1mnc 1zp5 1zs0 1zvx 2oy2 2oy4 3dng 3dpe 3dpf 3tt4 5h8x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QKZ)