1LDN

STRUCTURE OF A TERNARY COMPLEX OF AN ALLOSTERIC LACTATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 2.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.157 

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This is version 1.4 of the entry. See complete history


Literature

Structure of a ternary complex of an allosteric lactate dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution.

Wigley, D.B.Gamblin, S.J.Turkenburg, J.P.Dodson, E.J.Piontek, K.Muirhead, H.Holbrook, J.J.

(1992) J Mol Biol 223: 317-335

  • DOI: https://doi.org/10.1016/0022-2836(92)90733-z
  • Primary Citation of Related Structures:  
    1LDN

  • PubMed Abstract: 

    We report the refined structure of a ternary complex of an allosterically activated lactate dehydrogenase, including the important active site loop. Eightfold non-crystallographic symmetry averaging was utilized to improve the density maps. Interactions between the protein and bound coenzyme and oxamate are described in relation to other studies using site-specific mutagenesis. Fructose 1,6-bisphosphate (FruP2) is bound to the enzyme across one of the 2-fold axes of the tetramer, with the two phosphate moieties interacting with two anion binding sites, one on each of two subunits, across this interface. However, because FruP2 binds at this special site, yet does not possess an internal 2-fold symmetry axis, the ligand is statistically disordered and binds to each site in two different orientations. Binding of FruP2 to the tetramer is signalled to the active site principally through two interactions with His188 and Arg173. His188 is connected to His195 (which binds the carbonyl group of the substrate) and Arg173 is connected to Arg171 (the residue that binds the carboxylate group of the substrate).


  • Organizational Affiliation

    Department of Biochemistry, University of Leicester, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-LACTATE DEHYDROGENASE
A, B, C, D, E
A, B, C, D, E, F, G, H
316Geobacillus stearothermophilusMutation(s): 0 
EC: 1.1.1.27
UniProt
Find proteins for P00344 (Geobacillus stearothermophilus)
Explore P00344 
Go to UniProtKB:  P00344
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00344
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
BA [auth H]
K [auth A]
N [auth B]
P [auth C]
R [auth D]
BA [auth H],
K [auth A],
N [auth B],
P [auth C],
R [auth D],
U [auth E],
X [auth F],
Z [auth G]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
FBP
Query on FBP

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
S [auth E],
V [auth F]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
OXM
Query on OXM

Download Ideal Coordinates CCD File 
AA [auth H]
J [auth A]
M [auth B]
O [auth C]
Q [auth D]
AA [auth H],
J [auth A],
M [auth B],
O [auth C],
Q [auth D],
T [auth E],
W [auth F],
Y [auth G]
OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.9α = 90
b = 118.2β = 96.07
c = 135.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Structure summary