2B5M Dna Binding Protein Protein Binding date Sep 28, 2005
title Crystal Structure Of Ddb1
authors T.Li, X.Chen, K.C.Garbutt, P.Zhou, N.Zheng
compound source
Molecule: Damage-Specific Dna Binding Protein 1
Chain: A
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
symmetry Space Group: P 21 21 21
R_factor 0.232 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.380 133.834 184.715 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.92 Å
Gene
Ontology
ChainFunctionProcessComponent
A


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] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (2b5m.pdb1.gz) 175 Kb
  • CSU: Contacts of Structural Units for 2B5M
  • Likely Quarternary Molecular Structure file(s) for 2B5M
  • Structure Factors (252 Kb)
  • Retrieve 2B5M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2B5M from S2C, [Save to disk]
  • Re-refined 2b5m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2B5M 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 2B5M
  • 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 2B5M, from MSDmotif at EBI
  • Fold representative 2b5m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2b5m_A] [2b5m]
  • SWISS-PROT database: [Q16531]
  • Domain organization of [DDB1_HUMAN] by SWISSPFAM
  • Other resources with information on 2B5M
  • Community annotation for 2B5M 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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