1Y9A

Alcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of alcohol dehydrogenase from Entamoeba histolytica.

Shimon, L.J.Goihberg, E.Peretz, M.Burstein, Y.Frolow, F.

(2006) Acta Crystallogr.,Sect.D 62: 541-547

  • DOI: 10.1107/S0907444906009292

  • PubMed Abstract: 
  • The structure of the apo form of alcohol dehydrogenase from a single-cell eukaryotic source, Entamoeba histolytica, has been determined at 1.8 A. To date, bacterial and archeal alcohol dehydrogenases, which are biologically active as tetramers, have ...

    The structure of the apo form of alcohol dehydrogenase from a single-cell eukaryotic source, Entamoeba histolytica, has been determined at 1.8 A. To date, bacterial and archeal alcohol dehydrogenases, which are biologically active as tetramers, have crystallized with tetramers in the asymmetric unit. However, the current structure has one independent dimer per asymmetric unit and the full tetramer is generated by application of the crystallographic twofold symmetry element. This structure reveals that many of the crystallization and cryoprotection components, such as cacodylate, ethylene glycol, zinc ions and acetate, have been incorporated. These crystallization solution elements are found within the molecule and at the packing interfaces as an integral part of the three-dimensional arrangements of the tetramers. In addition, an unexpected modification of aspartic acid to O-carboxysulfanyl-4-oxo-L-homoserine was found at residue 245.


    Related Citations: 
    • Thermophilic alcohol dehydrogenase from the mesophile Entamoeba histolytica: crystallization and preliminary
      Shimon, L.J.W.,Peretz, M.,Goihberg, E.,Burstein, Y.,Frolow, F.
      (2002) Acta Crystallogr.,Sect.D 58: 546


    Organizational Affiliation

    Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel. linda.shimon@weizmann.ac.il




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADP-dependent alcohol dehydrogenase
A, C
360Entamoeba histolyticaMutation(s): 0 
Gene Names: ADH1
EC: 1.1.1.80
Find proteins for P35630 (Entamoeba histolytica)
Go to UniProtKB:  P35630
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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A, C
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OHS
Query on OHS
A, C
L-PEPTIDE LINKINGC5 H7 N O6 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.126 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.891α = 90.00
b = 234.139β = 90.00
c = 96.241γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description