3I8E Protein Binding date Jul 09, 2009
title Crystal Structure Of Ddb1 In Complex With The H-Box Motif Of
authors T.Li, E.I.Robert, P.C.V.Breugel, M.Strubin, N.Zheng
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A, B
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: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Wd Repeat-Containing Protein 42a
Chain: C, D
Fragment: Residues 153-165
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.260 R_Free 0.338
length a length b length c angle alpha angle beta angle gamma
64.138 133.815 183.999 90.00 90.45 90.00
method X-Ray Diffractionresolution 3.40 Å
A, B

Primary referenceA promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery., Li T, Robert EI, van Breugel PC, Strubin M, Zheng N, Nat Struct Mol Biol. 2010 Jan;17(1):105-11. Epub 2009 Dec 6. PMID:19966799
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (3i8e.pdb1.gz) 179 Kb
  • Biological Unit Coordinates (3i8e.pdb2.gz) 178 Kb
  • CSU: Contacts of Structural Units for 3I8E
  • Structure Factors (281 Kb)
  • Retrieve 3I8E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I8E from S2C, [Save to disk]
  • Re-refined 3i8e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3I8E 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 3I8E
  • 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 3I8E, from MSDmotif at EBI
  • Fold representative 3i8e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i8e] [3i8e_D] [3i8e_A] [3i8e_B] [3i8e_C]
  • SWISS-PROT database: [Q5TAQ9] [Q16531]
  • Domain organization of [DCAF8_HUMAN] [DDB1_HUMAN] by SWISSPFAM
  • Other resources with information on 3I8E
  • Community annotation for 3I8E 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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