3KB6

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).

Antonyuk, S.V.Strange, R.W.Ellis, M.J.Bessho, Y.Kuramitsu, S.Inoue, Y.Yokoyama, S.Hasnain, S.S.

(2009) Acta Crystallogr.,Sect.F 65: 1209-1213

  • DOI: 10.1107/S1744309109044935

  • PubMed Abstract: 
  • The crystal structure of D-lactate dehydrogenase from Aquifex aeolicus (aq_727) was determined to 2.12 A resolution in space group P2(1)2(1)2(1), with unit-cell parameters a = 90.94, b = 94.43, c = 188.85 A. The structure was solved by molecular repl ...

    The crystal structure of D-lactate dehydrogenase from Aquifex aeolicus (aq_727) was determined to 2.12 A resolution in space group P2(1)2(1)2(1), with unit-cell parameters a = 90.94, b = 94.43, c = 188.85 A. The structure was solved by molecular replacement using the coenzyme-binding domain of Lactobacillus helveticus D-lactate dehydrogenase and contained two homodimers in the asymmetric unit. Each subunit of the homodimer was found to be in a ;closed' conformation with the NADH cofactor bound to the coenzyme-binding domain and with a lactate (or pyruvate) molecule bound at the interdomain active-site cleft.


    Organizational Affiliation

    Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-lactate dehydrogenase
A, B, C, D
334Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: ldhA
Find proteins for O66939 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66939
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAC
Query on LAC

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Download CCD File 
A, B, C, D
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PPI
Query on PPI

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Download CCD File 
A, B, C, D
PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
A, B, C
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.938α = 90.00
b = 94.432β = 90.00
c = 188.849γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Advisory, Refinement description