3TDK Oxidoreductase date Aug 11, 2011
title Crystal Structure Of Human Udp-Glucose Dehydrogenase
authors V.Rajakannan, C.Han, R.Robinson
compound source
Molecule: Udp-Glucose 6-Dehydrogenase
Chain: A, B, G, H, L, K, F, E, D, C, J, I
Fragment: Unp Residues 1-487
Synonym: Udp-Glc Dehydrogenase, Udp-Glcdh, Udpgdh
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ugdh
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.230 R_Free 0.261
length a length b length c angle alpha angle beta angle gamma
173.132 191.177 225.807 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand NAD, UPG enzyme Oxidoreductase E.C. BRENDA
F, A, J, K, E, B, H, C, D, I, G, L

Primary referenceStructural Basis of Cooperativity in Human UDP-Glucose Dehydrogenase., Rajakannan V, Lee HS, Chong SH, Ryu HB, Bae JY, Whang EY, Huh JW, Cho SW, Kang LW, Choe H, Robinson RC, PLoS One. 2011;6(10):e25226. Epub 2011 Oct 3. PMID:21984906
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1853 Kb) [Save to disk]
  • Biological Unit Coordinates (3tdk.pdb1.gz) 923 Kb
  • Biological Unit Coordinates (3tdk.pdb2.gz) 927 Kb
  • LPC: Ligand-Protein Contacts for 3TDK
  • CSU: Contacts of Structural Units for 3TDK
  • Structure Factors (2867 Kb)
  • Retrieve 3TDK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TDK from S2C, [Save to disk]
  • Re-refined 3tdk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3TDK 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 3TDK
  • 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 3TDK, from MSDmotif at EBI
  • Fold representative 3tdk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tdk_K] [3tdk_B] [3tdk_D] [3tdk] [3tdk_H] [3tdk_F] [3tdk_I] [3tdk_J] [3tdk_G] [3tdk_A] [3tdk_E] [3tdk_L] [3tdk_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3TDK: [UDPG_MGDP_dh_C ] by SMART
  • Other resources with information on 3TDK
  • Community annotation for 3TDK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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