3E0C Dna Binding Protein date Jul 31, 2008
title Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
authors M.F.Amaya, L.Xu, H.Hao, C.Bountra, M.Wickstroem, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, Structural Genomics Consortiu
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A
Synonym: Damage-Specific Dna-Binding Protein 1, Uv-Damaged Binding Factor, Ddb P127 Subunit, Dna Damage-Binding Protei Uv-Damaged Dna-Binding Protein 1, Uv-Ddb 1, Xeroderma Pigme Group E-Complementing Protein, Xpce, Xpe-Binding Factor, Xp X-Associated Protein 1, Xap-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1, Xap1
Expression_system: Baculovirus
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.607 124.153 167.822 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.41 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure and function of WD40 domain proteins., Xu C, Min J, Protein Cell. 2011 Mar;2(3):202-14. Epub 2011 Apr 6. PMID:21468892
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (162 Kb) [Save to disk]
  • Biological Unit Coordinates (3e0c.pdb1.gz) 156 Kb
  • CSU: Contacts of Structural Units for 3E0C
  • Likely Quarternary Molecular Structure file(s) for 3E0C
  • Structure Factors (391 Kb)
  • Retrieve 3E0C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3E0C from S2C, [Save to disk]
  • Re-refined 3e0c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3E0C 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 3E0C
  • 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
  • 3D motif for 3E0C, from MSDmotif at EBI
  • Fold representative 3e0c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3e0c_A] [3e0c]
  • SWISS-PROT database: [Q16531]
  • Domain organization of [DDB1_HUMAN] by SWISSPFAM
  • Other resources with information on 3E0C
  • Community annotation for 3E0C at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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