6E8Y Oxidoreductase date Jul 31, 2018
title Unliganded Human Glycerol 3-Phosphate Dehydrogenase
authors L.S.Mydy, A.M.Gulick
compound source
Molecule: Glycerol-3-Phosphate Dehydrogenase [Nad(+)], Cyto
Chain: A, B
Synonym: Gpdh-C
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gpd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.170 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
63.370 76.160 64.390 90.00 96.03 90.00
method X-Ray Diffractionresolution 1.85 Å
enzyme Oxidoreductase E.C. BRENDA
A, B

Primary referenceHuman Glycerol 3-Phosphate Dehydrogenase: X-Ray Crystal Structures that Guide the Interpretation of Mutagenesis Studies., Mydy LS, Cristobal JR, Katigbak RD, Bauer P, Reyes AC, Kamerlin SCL, Richard JP, Gulick AM, Biochemistry. 2019 Jan 14. doi: 10.1021/acs.biochem.8b01103. PMID:30640445
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (6e8y.pdb1.gz) 206 Kb
  • CSU: Contacts of Structural Units for 6E8Y
  • Structure Factors (2158 Kb)
  • Retrieve 6E8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6E8Y from S2C, [Save to disk]
  • View 6E8Y 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 6E8Y
  • 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
  • Fold representative 6e8y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6e8y_A] [6e8y_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6E8Y
  • Community annotation for 6E8Y at PDBWiki (http://pdbwiki.org)

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