3PTF	Ligase	date	Dec 02, 2010
title	X-Ray Structure Of The Non-Covalent Complex Between Ubch5a A Ubiquitin
authors	I.Bosanac, S.G.Hymowitz
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 D1 Chain: A, B Fragment: E2 Synonym: Stimulator Of Fe Transport, Sft, Ubc45 Homolog, U Ubiquitin Carrier Protein D1, Ubiquitin-Conjugating Enzyme 1, Ubiquitin-Conjugating Enzyme E2-17 Kda 1, Ubiquitin-Prot D1; Ec: 6.3.2.19 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Sft, Ubc5a, Ubch5, Ubch5a, Ube2d1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Codonplus(De3)-Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-15b
Molecule: Polyubiquitin-B Chain: C, D Fragment: Ubiquitin Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ubiquitin Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21-Codonplus(De3)-Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-15b
symmetry	Space Group: P 21 21 21	R_factor 0.209 R_Free 0.275
crystal cell	length a length b length c angle alpha angle beta angle gamma 27.462 102.903 159.806 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand		enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Modulation of K11-Linkage Formation by Variable Loop Residues within UbcH5A., Bosanac I, Phu L, Pan B, Zilberleyb I, Maurer B, Dixit VM, Hymowitz SG, Kirkpatrick DS, J Mol Biol. 2011 May 6;408(3):420-31. Epub 2011 Mar 10. PMID:21396940

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk] Biological Unit Coordinates (3ptf.pdb1.gz) 73 Kb Biological Unit Coordinates (3ptf.pdb2.gz) 74 Kb CSU: Contacts of Structural Units for 3PTF Structure Factors (99 Kb) Retrieve 3PTF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3PTF from S2C, [Save to disk] Re-refined 3ptf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3PTF 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 3PTF

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 3D motif for 3PTF, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ptf_D] [3ptf_B] [3ptf_C] [3ptf] [3ptf_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3PTF: [UBCc] [UBQ ] by SMART

Other resources with information on 3PTF

Community annotation for 3PTF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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

---