1YDE Oxidoreductase date Dec 23, 2004
title Crystal Structure Of Human Retinal Short-Chain Dehydrogenase
authors P.Lukacik, G.Bunkozci, K.Kavanagh, M.Sundstrom, C.Arrowsmith, A.E F.Von Delft, U.Oppermann, Structural Genomics Consortium (Sgc
compound source
Molecule: Retinal Dehydrogenasereductase 3
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: P11
Expression_system_plasmid: Retsdr3a-P11
symmetry Space Group: P 1 21 1
R_factor 0.181 R_Free 0.229
length a length b length c angle alpha angle beta angle gamma
167.115 98.823 167.463 90.00 115.87 90.00
method X-Ray Diffractionresolution 2.40 Å
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G

Primary referenceStructural and biochemical characterization of human orphan DHRS10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity., Lukacik P, Keller B, Bunkoczi G, Kavanagh KL, Lee WH, Adamski J, Oppermann U, Biochem J. 2007 Mar 15;402(3):419-27. PMID:17067289
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (598 Kb) [Save to disk]
  • Biological Unit Coordinates (1yde.pdb1.gz) 154 Kb
  • Biological Unit Coordinates (1yde.pdb2.gz) 155 Kb
  • Biological Unit Coordinates (1yde.pdb3.gz) 153 Kb
  • Biological Unit Coordinates (1yde.pdb4.gz) 146 Kb
  • CSU: Contacts of Structural Units for 1YDE
  • Likely Quarternary Molecular Structure file(s) for 1YDE
  • Structure Factors (1498 Kb)
  • Retrieve 1YDE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YDE from S2C, [Save to disk]
  • Re-refined 1yde structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YDE 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 1YDE
  • 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
  • 3D motif for 1YDE, from MSDmotif at EBI
  • Fold representative 1yde from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yde_A] [1yde_G] [1yde_H] [1yde_M] [1yde_I] [1yde_K] [1yde_D] [1yde_L] [1yde_B] [1yde_J] [1yde_F] [1yde_O] [1yde_P] [1yde] [1yde_C] [1yde_E] [1yde_N]
  • SWISS-PROT database: [Q9BPX1]
  • Domain organization of [DHB14_HUMAN] by SWISSPFAM
  • Other resources with information on 1YDE
  • Community annotation for 1YDE 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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