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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX MMP-8/BF471 (CATECHOL INHIBITOR)
 
Authors :  G. Pochetti, R. Montanari, D. Capelli, P. Tortorella
Date :  24 Dec 15  (Deposition) - 02 Nov 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Catechol Function, Mmps, Inhibitor, Metalloprotese, Zinc Binding Function, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tauro, A. Laghezza, F. Loiodice, L. Piemontese, A. Caradonna, D. Capelli, R. Montanari, G. Pochetti, A. Di Pizio, M. Agamennone, C. Campestre, P. Tortorella
Catechol-Based Matrix Metalloproteinase Inhibitors With Additional Antioxidative Activity.
J Enzyme Inhib Med Chem V. 31 25 2016
PubMed-ID: 27556138  |  Reference-DOI: 10.1080/14756366.2016.1217853

(-) Compounds

Molecule 1 - NEUTROPHIL COLLAGENASE
    Chains: A
    EC Number: 3.4.24.34
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MMP8, CLG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MATRIX 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  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
15XT1Ligand/Ion~{N}-[3,4-BIS(OXIDANYL)PHENYL]-4-PHENYL-BENZENESULFONAMIDE
27FY1Ligand/Ion~{N}-[4,5-BIS(OXIDANYLIDENE)CYCLOHEXEN-1-YL]-4-PHENYL-BENZENESULFONAMIDE
3CA2Ligand/IonCALCIUM ION
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:137 , GLY A:169 , GLY A:171 , ASP A:173 , HOH A:416 , HOH A:456binding 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 , 5XT A:305 , 7FY A:306binding site for residue ZN A 304
5AC5SOFTWAREGLY A:158 , ILE A:159 , LEU A:160 , ALA A:161 , HIS A:162 , ALA A:163 , LEU A:193 , VAL A:194 , HIS A:197 , GLU A:198 , HIS A:201 , LEU A:214 , PRO A:217 , ASN A:218 , TYR A:219 , ALA A:220 , ARG A:222 , ZN A:304 , 7FY A:306 , HOH A:403 , HOH A:412 , HOH A:428 , HOH A:458 , HOH A:503binding site for residue 5XT A 305
6AC6SOFTWAREGLY A:158 , ILE A:159 , LEU A:160 , ALA A:161 , HIS A:162 , LEU A:193 , VAL A:194 , HIS A:197 , GLU A:198 , HIS A:201 , HIS A:207 , LEU A:214 , PRO A:217 , ASN A:218 , TYR A:219 , ALA A:220 , ARG A:222 , ZN A:304 , 5XT A:305 , HOH A:403 , HOH A:412 , HOH A:428 , HOH A:458 , HOH A:503binding site for residue 7FY A 306
7AC7SOFTWAREALA A:112 , ASP A:115 , SER A:186 , PHE A:192 , THR A:224 , ASN A:226 , TYR A:227 , HOH A:411 , HOH A:438 , HOH A:489 , HOH A:513binding site for residue MES A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H8X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H8X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H8X)

(-) Exons   (0, 0)

(no "Exon" information available for 5H8X)

(-) 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: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
                 5h8x A  80 MLTPGNPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG 242
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   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 5H8X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H8X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H8X)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5h8x)
 

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  5h8x
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  MMP8_HUMAN | P22894
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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP8_HUMAN | P22894: 1a85 1a86 1bzs 1i73 1i76 1jan 1jao 1jap 1jaq 1jh1 1jj9 1kbc 1mmb 1mnc 1zp5 1zs0 1zvx 2oy2 2oy4 3dng 3dpe 3dpf 3tt4 4qkz

(-) Related Entries Specified in the PDB File

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