5D1M	Ligase	date	Oct 08, 2013
title	Crystal Structure Of Ubch5b In Complex With The Ring-U5br Fr Ao7 (P199a)
authors	Y.H.Liang, S.Li, A.M.Weissman, X.Ji
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 D2 Chain: A 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		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ube2d2, Pubc1, Ubc4, Ubc5b, Ubch4, Ubch5b Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Petduet
Molecule: E3 Ubiquitin-Protein Ligase Rnf25 Chain: B Fragment: Unp Residues 126-258 Synonym: Ring Finger Protein 25 Ec: 6.3.2.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rnf25 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Petduet
symmetry	Space Group: C 1 2 1	R_factor 0.188 R_Free 0.223
crystal cell	length a length b length c angle alpha angle beta angle gamma 105.696 47.415 67.975 90.00 118.32 90.00
method	X-Ray Diffraction	resolution	1.58 Å
ligand	EDO, OXL, PEG, ZN	enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A B
Primary reference	Insights into Ubiquitination from the Unique Clamp-like Binding of the RING E3 AO7 to the E2 UbcH5B., Li S, Liang YH, Mariano J, Metzger MB, Stringer DK, Hristova VA, Li J, Randazzo PA, Tsai YC, Ji X, Weissman AM, J Biol Chem. 2015 Dec 18;290(51):30225-39. doi: 10.1074/jbc.M115.685867. Epub, 2015 Oct 16. PMID:26475854

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk] Biological Unit Coordinates (5d1m.pdb1.gz) 54 Kb LPC: Ligand-Protein Contacts for 5D1M CSU: Contacts of Structural Units for 5D1M Structure Factors (310 Kb) Retrieve 5D1M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D1M from S2C, [Save to disk] Re-refined 5d1m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D1M 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 5D1M

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5d1m_A] [5d1m] [5d1m_B] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5D1M: [RING] [UBCc ] by SMART

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