2OY2 Hydrolase date Feb 21, 2007
title Human Mmp-8 In Complex With Peptide Iag
authors V.Calderone, I.Bertini, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo
compound source
Molecule: Neutrophil Collagenase
Chain: A, F
Fragment: Catalytic Domain
Synonym: Matrix Metalloproteinase-8, Mmp-8, Pmnl Collagenas Cl;
Ec: 3.4.24.34
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mmp8, Clg1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21

Molecule: Ile-Ala-Gly Peptide
Chain: W, Y
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.164 R_Free 0.192
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.207 68.533 78.281 90.00 98.10 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand CA, ZN enzyme Hydrolase E.C.3.4.24.34 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A


Primary referenceSnapshots of the reaction mechanism of matrix metalloproteinases., Bertini I, Calderone V, Fragai M, Luchinat C, Maletta M, Yeo KJ, Angew Chem Int Ed Engl. 2006 Dec 4;45(47):7952-5. PMID:17096442
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (2oy2.pdb1.gz) 59 Kb
  • Biological Unit Coordinates (2oy2.pdb2.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 2OY2
  • CSU: Contacts of Structural Units for 2OY2
  • Likely Quarternary Molecular Structure file(s) for 2OY2
  • Structure Factors (2669 Kb)
  • Retrieve 2OY2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OY2 from S2C, [Save to disk]
  • Re-refined 2oy2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OY2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2OY2
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2OY2, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oy2_F] [2oy2] [2oy2_Y] [2oy2_A] [2oy2_W]
  • SWISS-PROT database: [P22894]
  • Domain organization of [MMP8_HUMAN] by SWISSPFAM
  • Domain found in 2OY2: [ZnMc ] by SMART
  • Other resources with information on 2OY2
  • Community annotation for 2OY2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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