2AFB Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from THERMOTOGA MARITIMA at 2.05 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.23
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.05
ligand CA, MSE, NI enzyme
note 2AFB supersedes 1J5V
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution., Mathews II, McMullan D, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Rife CL, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Weekes D, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA, Proteins. 2007 Nov 14;70(2):603-608. PMID:18004772
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (2afb.pdb1.gz) 318 Kb
  • LPC: Ligand-Protein Contacts for 2AFB
  • CSU: Contacts of Structural Units for 2AFB
  • Likely Quarternary Molecular Structure file(s) for 2AFB
  • Structure Factors (6985 Kb)
  • Retrieve 2AFB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2AFB from S2C, [Save to disk]
  • Re-refined 2afb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2AFB 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 2AFB
  • 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
  • 3D motif for 2AFB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2afb] [2afb_A] [2afb_B]
  • SWISS-PROT database: [Q9WXS2]
  • Domain organization of [Q9WXS2_THEMA] by SWISSPFAM
  • Other resources with information on 2AFB
  • Community annotation for 2AFB 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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