2IBI Hydrolase date Sep 11, 2006
title Covalent Ubiquitin-Usp2 Complex
authors J.R.Walker, G.V.Avvakumov, G.Bernstein, S.Xue, P.J.Finerty Jr., F.Mackenzie, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc)
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 2
Chain: A
Fragment: Catalytic Domain, Residues 251-605
Synonym: Ubiquitin Thioesterase 2, Ubiquitin-Specific- Processing Protease 2, Deubiquitinating Enzyme 2, 41 Kda Ubiquitin-Specific Protease;
Ec: 3.1.2.15
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp2, Ubp41
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Lic

Molecule: Ubiquitin
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps27a, Uba52, Ubb, Ubc
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptby2
symmetry Space Group: C 1 2 1
R_factor 0.190 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.839 54.400 75.021 90.00 107.66 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand NEH, ZN enzyme Hydrolase E.C.3.1.2.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (2ibi.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 2IBI
  • CSU: Contacts of Structural Units for 2IBI
  • Likely Quarternary Molecular Structure file(s) for 2IBI
  • Structure Factors (319 Kb)
  • Retrieve 2IBI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IBI from S2C, [Save to disk]
  • Re-refined 2ibi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IBI 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 2IBI
  • 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 2IBI, from MSDmotif at EBI
  • Fold representative 2ibi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ibi] [2ibi_B] [2ibi_A]
  • SWISS-PROT database: [P62988] [O75604]
  • Domain organization of [UBIQ_HUMAN] [UBP2_HUMAN] by SWISSPFAM
  • Domain found in 2IBI: [UBQ ] by SMART
  • Other resources with information on 2IBI
  • Community annotation for 2IBI 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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