5JK7	Viral Protein Dna Binding Protein	date	Apr 26, 2016
title	The X-Ray Structure Of The Ddb1-Dcaf1-Vpr-Ung2 Complex
authors	G.Calero, J.Ahn, Y.Wu
compound		source
Molecule: Dna Damage-Binding Protein 1 Chain: A, B Synonym: Ddb P127 Subunit,Dna Damage-Binding Protein A,Ddba Specific Dna-Binding Protein 1,Hbv X-Associated Protein 1,X Damaged Dna-Binding Factor,Uv-Damaged Dna-Binding Protein 1 Xpe-Binding Factor,Xpe-Bf,Xeroderma Pigmentosum Group E-Com Protein,Xpce; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ddb1, Xap1 Expression_system: Insect Cell Expression Vector Ptie1 Expression_system_taxid: 266783
Molecule: Protein Vprbp Chain: C, E Fragment: Unp Residues 1045-1396 Synonym: Ddb1- And Cul4-Associated Factor 1,Hiv-1 Vpr-Bindi Protein,Vprbp,Serinethreonine-Protein Kinase Vprbp,Vpr-Int Protein; Ec: 2.7.11.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vprbp, Dcaf1, Kiaa0800, Rip Expression_system: Insect Cell Expression Vector Ptie1 Expression_system_taxid: 266783
Molecule: Uracil-Dna Glycosylase Chain: D, G Fragment: Unp Residues 85-304 Synonym: Udg Ec: 3.2.2.27 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ung, Dgu, Ung1, Ung15 Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4; Expression_system_taxid: 1182032
Molecule: Protein Vpr Chain: F, H Synonym: R Orf Protein,Viral Protein R Engineered: Yes		Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B (Isolate Ny5); Organism_common: Hiv-1 Organism_taxid: 11698 Strain: Isolate Ny5 Gene: Vpr Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4; Expression_system_taxid: 1182032
symmetry	Space Group: P 1	R_factor 0.176 R_Free 0.207
crystal cell	length a length b length c angle alpha angle beta angle gamma 119.900 128.200 129.200 75.11 89.44 65.37
method	X-Ray Diffraction	resolution	3.49 Å
ligand		enzyme	Transferase E.C.2.7.11.1 BRENDA
Gene Ontology	Chain Function Process Component A, B D, G E, C F, H
Primary reference	The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction., Wu Y, Zhou X, Barnes CO, DeLucia M, Cohen AE, Gronenborn AM, Ahn J, Calero G, Nat Struct Mol Biol. 2016 Aug 29. doi: 10.1038/nsmb.3284. PMID:27571178

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1187 Kb) [Save to disk] Biological Unit Coordinates (5jk7.pdb1.gz) 598 Kb Biological Unit Coordinates (5jk7.pdb2.gz) 590 Kb CSU: Contacts of Structural Units for 5JK7 Structure Factors (2135 Kb) Retrieve 5JK7 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5JK7 from S2C, [Save to disk] Re-refined 5jk7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5JK7 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 5JK7

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: [5jk7_D] [5jk7_G] [5jk7_C] [5jk7_A] [5jk7_E] [5jk7_B] [5jk7_H] [5jk7_F] [5jk7] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5JK7: [UDG] [UreE_C ] by SMART

Other resources with information on 5JK7

Community annotation for 5JK7 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

---