5A3D Dna Binding Protein date May 28, 2015
title Structural Insights Into The Recognition Of Cisplatin And Aa Lesions By Rad14 (Xpa)
authors J.Kuper, S.C.Koch, K.L.Gasteiger, N.Wichlein, S.Schneider, C.Kisk T.Carell
compound source
Molecule: Dna Repair Protein Rad14
Chain: A, B
Fragment: Dna Binding Domain
Synonym: Rad14
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Ppsg-Iba3

Molecule: 5'-D(Dtpcptpcptpapc 8fgptpcpaptpcpda
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Dg 5iupgpa 5iupgpapcpg 5iupapgpap 3';
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41
R_factor 0.210 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.727 53.727 130.551 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 5IU, 8FG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA)., Koch SC, Kuper J, Gasteiger KL, Simon N, Strasser R, Eisen D, Geiger S, Schneider S, Kisker C, Carell T, Proc Natl Acad Sci U S A. 2015 Jun 22. pii: 201508509. PMID:26100901
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (137 Kb) [Save to disk]
  • Biological Unit Coordinates (5a3d.pdb1.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 5A3D
  • CSU: Contacts of Structural Units for 5A3D
  • Structure Factors (464 Kb)
  • Retrieve 5A3D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5A3D from S2C, [Save to disk]
  • Re-refined 5a3d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5A3D 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 5A3D
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5a3d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5a3d_A] [5a3d] [5a3d_B] [5a3d_D] [5a3d_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5A3D
  • Community annotation for 5A3D at PDBWiki (http://pdbwiki.org)

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