3KB6 image
Deposition Date 2009-10-20
Release Date 2009-11-10
Last Version Date 2023-11-15
Entry Detail
PDB ID:
3KB6
Keywords:
OXIDOREDUCTASE
Title:
Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid
Biological Source:
Source Organism:
Aquifex aeolicus (Taxon ID: 63363)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.12 Å
R-Value Free:
0.21
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
3KB6 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:D-lactate dehydrogenase
Gene (Uniprot):ldhA
Chain IDs:A, B, C, D
Chain Length:334
Number of Molecules:4
Biological Source:Aquifex aeolicus
UniProt ID:O66939 Pfam ID:PF00389, PF02826 EC:1.1.1.28
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET SELENOMETHIONINE
Ligand Molecules
1PE
GOL
LAC
NAD
PEG
PPI
Primary Citation
Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).
Acta Crystallogr.,Sect.F 65 1209 1213 (2009)
PMID: 20054113 DOI: 10.1107/S1744309109044935

Abstact

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.

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Primary Citation of related structures
3KB6