3VON Hydrolase Ligase date Jan 30, 2012
title Crystalstructure Of The Ubiquitin Protease
authors Y.Sato, S.Fukai
compound source
Molecule: Ubiquitin Thioesterase Otub1
Chain: A, H, O, V, c, j
Fragment: Unp Residues 45-271
Synonym: Deubiquitinating Enzyme Otub1, Otu Domain-Containi Ubiquitin Aldehyde-Binding Protein 1, Otubain-1, Hotu1, Ubi Specific-Processing Protease Otub1;
Ec: 3.4.19.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hspc263, Otb1, Otu1, Otub1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: Ubiquitin-Conjugating Enzyme E2 Variant 2
Chain: B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o
Fragment: Unp Residues 6-143
Synonym: Ddvit 1, Enterocyte Differentiation-Associated Fac Edaf-1, Enterocyte Differentiation-Promoting Factor 1, Edpf Homolog, Vitamin D3-Inducible Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mms2, Ube2v2, Uev2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: Ubiquitin-Conjugating Enzyme E2 N
Chain: C, E, G, J, L, N, Q, S, U, X, Z, b, e, g, I, l, n, p
Fragment: Unp Residues 3-150
Synonym: Bendless-Like Ubiquitin-Conjugating Enzyme, Ubc13, Carrier Protein N, Ubiquitin-Protein Ligase N;
Ec: 6.3.2.19
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Blu, Ubc13, Ube2n
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.064 137.285 257.109 90.00 90.03 90.00
method X-Ray Diffractionresolution 3.15 Å
ligand
enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
S, N, E, Z, g, e, J, b, G, U, Q, C, L, i, n, X, l, p


a, T, K, d, Y, k, W, B, D, I, F, h, M, f, P, m, R, o


j, H, c, V, A, O


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2207 Kb) [Save to disk]
  • Biological Unit Coordinates (3von.pdb1.gz) 180 Kb
  • Biological Unit Coordinates (3von.pdb2.gz) 108 Kb
  • Biological Unit Coordinates (3von.pdb3.gz) 106 Kb
  • Biological Unit Coordinates (3von.pdb4.gz) 184 Kb
  • Biological Unit Coordinates (3von.pdb5.gz) 106 Kb
  • Biological Unit Coordinates (3von.pdb6.gz) 105 Kb
  • Biological Unit Coordinates (3von.pdb7.gz) 182 Kb
  • Biological Unit Coordinates (3von.pdb8.gz) 107 Kb
  • Biological Unit Coordinates (3von.pdb9.gz) 106 Kb
  • CSU: Contacts of Structural Units for 3VON
  • Structure Factors (1822 Kb)
  • Retrieve 3VON in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VON from S2C, [Save to disk]
  • Re-refined 3von structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VON 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 3VON
  • 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 3VON, from MSDmotif at EBI
  • Fold representative 3von from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3von_P] [3von_R] [3von_Q] [3von_e] [3von_o] [3von_W] [3von_A] [3von_i] [3von_n] [3von_g] [3von_l] [3von_S] [3von_b] [3von_M] [3von_L] [3von_U] [3von] [3von_H] [3von_X] [3von_F] [3von_T] [3von_G] [3von_K] [3von_f] [3von_m] [3von_d] [3von_c] [3von_V] [3von_k] [3von_J] [3von_h] [3von_I] [3von_j] [3von_N] [3von_a] [3von_Z] [3von_O] [3von_C] [3von_B] [3von_E] [3von_D] [3von_Y] [3von_p]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VON: [UBCc ] by SMART
  • Other resources with information on 3VON
  • Community annotation for 3VON at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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