6SY1 Structural Genomics date Sep 26, 2019
title Crystal Structure Of The Human 2-Oxoadipate Dehydrogenase Dh
authors G.A.Bezerra, W.Foster, L.Shrestha, I.A.Pena, J.Coker, S.Kolker, B. F.Von Delft, A.Edwards, C.Arrowsmith, C.Bountra, W.W.Yue, Struct Genomics Consortium (Sgc)
compound source
Molecule: Probable 2-Oxoglutarate Dehydrogenase E1 Componen Mitochondrial;
Chain: A, B
Synonym: Dehydrogenase E1 And Transketolase Domain-Containi 1;
Ec: 1.2.4.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dhtkd1, Kiaa1630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.190 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.550 81.220 86.900 63.43 76.96 72.06
method X-Ray Diffractionresolution 1.87 Å
ligand MG, TPP enzyme Oxidoreductase E.C.1.2.4.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism., Bezerra GA, Foster WR, Bailey HJ, Hicks KG, Sauer SW, Dimitrov B, McCorvie TJ, Okun JG, Rutter J, Kolker S, Yue WW, IUCrJ. 2020 Jun 10;7(Pt 4):693-706. doi: 10.1107/S205225252000696X. eCollection, 2020 Jul 1. PMID:32695416
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (291 Kb) [Save to disk]
  • Biological Unit Coordinates (6sy1.pdb1.gz) 284 Kb
  • LPC: Ligand-Protein Contacts for 6SY1
  • CSU: Contacts of Structural Units for 6SY1
  • Structure Factors (4649 Kb)
  • Retrieve 6SY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6SY1 from S2C, [Save to disk]
  • View 6SY1 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 6SY1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6sy1_A] [6sy1_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6SY1
  • Community annotation for 6SY1 at PDBWiki (http://pdbwiki.org)

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