2B5L Protein Binding Viral Protein date Sep 28, 2005
title Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V Protein
authors T.Li, X.Chen, K.C.Garbutt, P.Zhou, N.Zheng
compound source
Molecule: Damage-Specific Dna Binding Protein 1
Chain: A, B
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus

Molecule: Nonstructural Protein V
Chain: C, D
Engineered: Yes

Organism_scientific: Simian Virus 5
Organism_taxid: 11207
Gene: Pv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.299
length a length b length c angle alpha angle beta angle gamma
62.758 240.792 117.177 90.00 101.79 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand ZN enzyme
A, B

D, C

Primary referenceStructure of DDB1 in complex with a paramyxovirus V protein: viral hijack of a propeller cluster in ubiquitin ligase., Li T, Chen X, Garbutt KC, Zhou P, Zheng N, Cell. 2006 Jan 13;124(1):105-17. PMID:16413485
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (393 Kb) [Save to disk]
  • Biological Unit Coordinates (2b5l.pdb1.gz) 194 Kb
  • Biological Unit Coordinates (2b5l.pdb2.gz) 196 Kb
  • LPC: Ligand-Protein Contacts for 2B5L
  • CSU: Contacts of Structural Units for 2B5L
  • Likely Quarternary Molecular Structure file(s) for 2B5L
  • Structure Factors (675 Kb)
  • Retrieve 2B5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2B5L from S2C, [Save to disk]
  • Re-refined 2b5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2B5L 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 2B5L
  • 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 2B5L, from MSDmotif at EBI
  • Fold representative 2b5l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2b5l_C] [2b5l_B] [2b5l_A] [2b5l] [2b5l_D]
  • SWISS-PROT database: [Q16531] [P11207]
  • Domain organization of [DDB1_HUMAN] [V_SV5] by SWISSPFAM
  • Other resources with information on 2B5L
  • Community annotation for 2B5L 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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