5FER	Ligase	date	Dec 17, 2015
title	Complex Of Trim25 Ring With Ubch5-Ub
authors	K.Rittinger, M.G.Koliopoulos, D.Esposito
compound		source
Molecule: E3 Ubiquitinisg15 Ligase Trim25 Chain: A, D Synonym: Estrogen-Responsive Finger Protein,Ring Finger Pro Ring-Type E3 Ubiquitin Transferase,Tripartite Motif-Contain Protein 25,Ubiquitinisg15-Conjugating Enzyme Trim25,Zinc F Protein 147; Ec: 6.3.2.-,2.3.2.27 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Trim25, Efp, Rnf147, Znf147 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-Conjugating Enzyme E2 D1 Chain: B, E Synonym: (E3-Independent) E2 Ubiquitin-Conjugating Enzyme D Ubiquitin-Conjugating Enzyme D1,Stimulator Of Fe Transport, Homolog,Ubch5,Ubiquitin Carrier Protein D1,Ubiquitin-Conjug Enzyme E2(17)Kb 1,Ubiquitin-Conjugating Enzyme E2-17 Kda 1, Protein Ligase D1; Ec: 2.3.2.23,2.3.2.24 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ube2d1, Sft, Ubc5a, Ubch5, Ubch5a Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-40s Ribosomal Protein S27a Chain: C, F Synonym: Ubiquitin Carboxyl Extension Protein 80		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
symmetry	Space Group: P 21 21 21	R_factor 0.227 R_Free 0.273
crystal cell	length a length b length c angle alpha angle beta angle gamma 60.480 71.700 160.430 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.34 Å
ligand	ZN	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component E, B
Primary reference	Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity., Koliopoulos MG, Esposito D, Christodoulou E, Taylor IA, Rittinger K, EMBO J. 2016 May 6. pii: e201593741. PMID:27154206

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk] Biological Unit Coordinates (5fer.pdb1.gz) 99 Kb LPC: Ligand-Protein Contacts for 5FER CSU: Contacts of Structural Units for 5FER Structure Factors (641 Kb) Retrieve 5FER in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5FER from S2C, [Save to disk] Re-refined 5fer structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5FER 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 5FER

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: [5fer_D] [5fer_B] [5fer] [5fer_C] [5fer_E] [5fer_A] [5fer_F] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5FER: [RING] [UBCc] [UBQ ] by SMART

Other resources with information on 5FER

Community annotation for 5FER at PDBWiki (http://pdbwiki.org)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---