2VFJ Hydrolase date Nov 04, 2007
title Structure Of The A20 Ovarian Tumour (Otu) Domain
authors D.Komander, D.Barford
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C, D
Fragment: Ovarian Tumour (Otu) Domain, Residues 1-366
Synonym: Alpha-Induced Protein 3, Dna-Binding Protein A20, Zinc Finger Protein A20;
Ec: 3.4.19.12
Engineered: Yes
Other_details: Residues 1-366
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_plasmid: Pgex6p1
symmetry Space Group: P 1 21 1
R_factor 0.2044 R_Free 0.2429
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.964 83.023 164.940 90.00 98.08 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand MG, SO4 enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure of the A20 OTU domain and mechanistic insights into deubiquitination., Komander D, Barford D, Biochem J. 2007 Oct 26;. PMID:17961127
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (449 Kb) [Save to disk]
  • Biological Unit Coordinates (2vfj.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (2vfj.pdb2.gz) 110 Kb
  • Biological Unit Coordinates (2vfj.pdb3.gz) 114 Kb
  • Biological Unit Coordinates (2vfj.pdb4.gz) 115 Kb
  • LPC: Ligand-Protein Contacts for 2VFJ
  • CSU: Contacts of Structural Units for 2VFJ
  • Likely Quarternary Molecular Structure file(s) for 2VFJ
  • Structure Factors (265 Kb)
  • Retrieve 2VFJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VFJ from S2C, [Save to disk]
  • Re-refined 2vfj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VFJ 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 2VFJ
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2VFJ, from MSDmotif at EBI
  • Fold representative 2vfj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vfj_B] [2vfj_D] [2vfj_A] [2vfj_C] [2vfj]
  • SWISS-PROT database: [P21580]
  • Domain organization of [TNAP3_HUMAN] by SWISSPFAM
  • Other resources with information on 2VFJ
  • Community annotation for 2VFJ 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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