3HCU Signaling Protein Ligase date May 06, 2009
title Crystal Structure Of Traf6 In Complex With Ubc13 In The C2 S
authors Q.Yin, S.C.Lin, B.Lamothe, M.Lu, Y.C.Lo, G.Hura, L.Zheng, R.L.Ric A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, H.Wu
compound source
Molecule: Tnf Receptor-Associated Factor 6
Chain: A, C
Fragment: Ring And Zinc Finger 1: Unp Residues 50-159
Synonym: Interleukin-1 Signal Transducer, Ring Finger Prote
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnf85, Traf6
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codon-Plus Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Ubiquitin-Conjugating Enzyme E2 N
Chain: B, D
Fragment: Ubc13
Synonym: Ubiquitin-Protein Ligase N, Ubiquitin Carrier Prot Ubc13, Bendless-Like Ubiquitin-Conjugating Enzyme;
Ec: 6.3.2.19
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Blu, Ube2n
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codon-Plus Ripl
Expression_system_vector_type: Plasmid
symmetry Space Group: C 1 2 1
R_factor 0.256 R_Free 0.333
crystal
cell
length a length b length c angle alpha angle beta angle gamma
130.493 41.387 123.745 90.00 116.20 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand ZN enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceE2 interaction and dimerization in the crystal structure of TRAF6., Yin Q, Lin SC, Lamothe B, Lu M, Lo YC, Hura G, Zheng L, Rich RL, Campos AD, Myszka DG, Lenardo MJ, Darnay BG, Wu H, Nat Struct Mol Biol. 2009 Jun;16(6):658-66. Epub 2009 May 24. PMID:19465916
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (3hcu.pdb1.gz) 44 Kb
  • Biological Unit Coordinates (3hcu.pdb2.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 3HCU
  • CSU: Contacts of Structural Units for 3HCU
  • Likely Quarternary Molecular Structure file(s) for 3HCU
  • Structure Factors (259 Kb)
  • Retrieve 3HCU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HCU from S2C, [Save to disk]
  • Re-refined 3hcu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HCU 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 3HCU
  • 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 3HCU, from MSDmotif at EBI
  • Fold representative 3hcu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hcu_D] [3hcu_B] [3hcu] [3hcu_C] [3hcu_A]
  • SWISS-PROT database: [Q9Y4K3] [P61088]
  • Domain organization of [TRAF6_HUMAN] [UBE2N_HUMAN] by SWISSPFAM
  • Domains found in 3HCU: [RING] [UBCc ] by SMART
  • Other resources with information on 3HCU
  • Community annotation for 3HCU 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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