5D0K	Ligase	date	Aug 03, 2015
title	Structure Of Ube2d2:Rnf165:Ub Complex
authors	J.D.Wright, C.L.Day, P.D.Mace
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 D2 Chain: A, D, G, J Synonym: Ubiquitin Carrier Protein D2,Ubiquitin-Conjugating E2(17)Kb 2,Ubiquitin-Conjugating Enzyme E2-17 Kda 2,Ubiquit Ligase D2,P53-Regulated Ubiquitin-Conjugating Enzyme 1; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ube2d2, Pubc1, Ubc4, Ubc5b, Ubch4, Ubch5b Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ring Finger Protein 165 Chain: C, F, I, L Fragment: Unp Residues 255-346 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rnf165 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Polyubiquitin-B Chain: B, E, H, K Fragment: Unp Residues 1-76 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubb Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 3	R_factor 0.192 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 113.046 113.046 135.667 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	ZN	enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A, J, D, G F, C, I, L
Primary reference	Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity., Wright JD, Mace PD, Day CL, Nat Struct Mol Biol. 2015 Dec 14. doi: 10.1038/nsmb.3142. PMID:26656854

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (400 Kb) [Save to disk] Biological Unit Coordinates (5d0k.pdb1.gz) 101 Kb Biological Unit Coordinates (5d0k.pdb2.gz) 100 Kb Biological Unit Coordinates (5d0k.pdb3.gz) 100 Kb Biological Unit Coordinates (5d0k.pdb4.gz) 100 Kb LPC: Ligand-Protein Contacts for 5D0K CSU: Contacts of Structural Units for 5D0K Structure Factors (3145 Kb) Retrieve 5D0K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D0K from S2C, [Save to disk] Re-refined 5d0k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D0K in 3D

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Visual 3D analysis of 5D0K

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5d0k_G] [5d0k_D] [5d0k_A] [5d0k_L] [5d0k_I] [5d0k] [5d0k_K] [5d0k_C] [5d0k_B] [5d0k_F] [5d0k_J] [5d0k_E] [5d0k_H] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5D0K: [RING] [UBCc] [UBQ ] by SMART

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