1YKF Oxidoreductase date Mar 25, 1996
title Nadp-Dependent Alcohol Dehydrogenase From Thermoanaerobium Brockii
authors Y.Korkhin, F.Frolow
compound source
Molecule: Nadp-Dependent Alcohol Dehydrogenase
Chain: A, B, C, D
Engineered: Yes
Other_details: Holo-Enzyme Form
Organism_scientific: Thermoanaerobacter Brockii
Organism_taxid: 29323
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Bacterium
symmetry Space Group: P 65
R_factor 0.215 R_Free 0.267
length a length b length c angle alpha angle beta angle gamma
80.614 80.614 400.335 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand NAP, ZN enzyme Oxidoreductase E.C. BRENDA
note 1YKF (Molecule of the Month:pdb13)
related structures by homologous chain: 1BXZ, 1QOR
A, D, C, B

Primary referenceNADP-dependent bacterial alcohol dehydrogenases: crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii., Korkhin Y, Kalb(Gilboa) AJ, Peretz M, Bogin O, Burstein Y, Frolow F, J Mol Biol. 1998 May 22;278(5):967-81. PMID:9836873
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (225 Kb) [Save to disk]
  • Biological Unit Coordinates (1ykf.pdb1.gz) 220 Kb
  • LPC: Ligand-Protein Contacts for 1YKF
  • CSU: Contacts of Structural Units for 1YKF
  • Likely Quarternary Molecular Structure file(s) for 1YKF
  • Retrieve 1YKF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YKF from S2C, [Save to disk]
  • View 1YKF 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 1YKF
  • 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 1YKF, from MSDmotif at EBI
  • Genome occurence of 1YKF's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ykfa1, region A:1-139,A:314-352 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfa2, region A:140-313 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfb1, region B:1-139,B:314-352 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfb2, region B:140-313 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfc1, region C:1-139,C:314-352 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfc2, region C:140-313 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfd1, region D:1-139,D:314-352 [Jmol] [rasmolscript] [script source]
        - Domain d1ykfd2, region D:140-313 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ykf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ykf_D] [1ykf_B] [1ykf_C] [1ykf] [1ykf_A]
  • SWISS-PROT database: [P14941]
  • Domain organization of [ADH_THEBR] by SWISSPFAM
  • Other resources with information on 1YKF
  • Community annotation for 1YKF at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1YKF from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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