3KHU Oxidoreductase date Oct 30, 2009
title Crystal Structure Of Human Udp-Glucose Dehydrogenase Glu161g Complex With Thiohemiacetal Intermediate
authors A.Chaikuad, S.Egger, W.W.Yue, K.Guo, R.Sethi, P.Filippakopoulos, J.R.C.Muniz, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.M.Edwards, K.L.Kavanagh, B.Nidetzky, U.Oppermann, Structural Consortium (Sgc)
compound source
Molecule: Udp-Glucose 6-Dehydrogenase
Chain: A, B, C, D, E, F
Fragment: Unp Residues 1-466
Synonym: Udp-Glc Dehydrogenase, Udp-Glcdh, Udpgdh
Ec: 1.1.1.22
Engineered: Yes
Mutation: 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)-R3-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pben1
symmetry Space Group: P 21 21 2
R_factor 0.195 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
203.540 207.340 93.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand EDO, EPE, UPG enzyme Oxidoreductase E.C.1.1.1.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructural and kinetic evidence that the catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates., Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B, J Biol Chem. 2011 Nov 28. PMID:22123821
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (490 Kb) [Save to disk]
  • Biological Unit Coordinates (3khu.pdb1.gz) 475 Kb
  • LPC: Ligand-Protein Contacts for 3KHU
  • CSU: Contacts of Structural Units for 3KHU
  • Structure Factors (8695 Kb)
  • Retrieve 3KHU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KHU from S2C, [Save to disk]
  • Re-refined 3khu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KHU 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 3KHU
  • 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 3KHU, from MSDmotif at EBI
  • Fold representative 3khu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3khu_A] [3khu_B] [3khu_D] [3khu_F] [3khu] [3khu_C] [3khu_E]
  • SWISS-PROT database: [O60701]
  • Domain organization of [UGDH_HUMAN] by SWISSPFAM
  • Domain found in 3KHU: [UDPG_MGDP_dh_C ] by SMART
  • Other resources with information on 3KHU
  • Community annotation for 3KHU 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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