1TFF Hydrolase date May 27, 2004
title Structure Of Otubain-2
authors M.H.Nanao, S.O.Tcherniuk, J.Chroboczek, O.Dideberg, A.Dessen, M.Y.Balakirev
compound source
Molecule: Ubiquitin Thiolesterase Protein Otub2
Chain: A
Fragment: Otubain-2
Synonym: Otubain 2, Otu Domain-Containing Ubiquitin Aldehyde-Binding Protein 2, Ubiquitin- Specific Processing Protease Otub2, Deubiquitinating Enzyme Otub2;
Ec: 3.4.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Otub2, Otb2, Otu2, C14orf137
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 21 21 21
R_factor 0.188 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.433 65.401 76.259 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand MSE enzyme Hydrolase E.C.3.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of human otubain 2., Nanao MH, Tcherniuk SO, Chroboczek J, Dideberg O, Dessen A, Balakirev MY, EMBO Rep 2004 Aug;5(8):783-8. Epub 2004 Jul 16. PMID:15258613
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1tff.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 1TFF
  • CSU: Contacts of Structural Units for 1TFF
  • Likely Quarternary Molecular Structure file(s) for 1TFF
  • Retrieve 1TFF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TFF from S2C, [Save to disk]
  • View 1TFF 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 1TFF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1TFF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tffa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1tff from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tff] [1tff_A]
  • SWISS-PROT database: [Q96DC9]
  • Domain organization of [OTUB2_HUMAN] by SWISSPFAM
  • Other resources with information on 1TFF
  • Community annotation for 1TFF 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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