4UB2 Transferase, Lyase Dna date Aug 11, 2014
title Dna Polymerase Beta Product Complex With A Templating Cytosi Oxodgmp, 120 S
authors B.D.Freudenthal, S.H.Wilson, W.A.Beard
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: 5'-D(Cpcpgpapcpcpgpcpgpcpaptpcpapg
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Gpcptpgpaptpgpcpgpcp(8og))-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Pgptpcpgpg)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.293
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.099 79.589 55.668 90.00 109.69 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand 8OG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUncovering the polymerase-induced cytotoxicity of an oxidized nucleotide., Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH, Nature. 2014 Nov 17. doi: 10.1038/nature13886. PMID:25409153
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (4ub2.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 4UB2
  • CSU: Contacts of Structural Units for 4UB2
  • Structure Factors (252 Kb)
  • Retrieve 4UB2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UB2 from S2C, [Save to disk]
  • Re-refined 4ub2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UB2 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 4UB2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4UB2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o4ub2, region B:1-103 [Jmol] [rasmolscript] [script source]
  • Fold representative 4ub2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ub2_D] [4ub2] [4ub2_A] [4ub2_P] [4ub2_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4UB2: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4UB2
  • Community annotation for 4UB2 at PDBWiki (http://pdbwiki.org)

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