1LDG | pdb_00001ldg

PLASMODIUM FALCIPARUM L-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE

• PDB DOI: https://doi.org/10.2210/pdb1LDG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-09-10 Released: 1997-09-17 
• Deposition Author(s): Dunn, C., Banfield, M., Barker, J., Higham, C., Moreton, K., Turgut-Balik, D., Brady, L., Holbrook, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

The structure of lactate dehydrogenase from Plasmodium falciparum reveals a new target for anti-malarial design.

Dunn, C.R., Banfield, M.J., Barker, J.J., Higham, C.W., Moreton, K.M., Turgut-Balik, D., Brady, R.L., Holbrook, J.J.

(1996) Nat Struct Biol 3: 912-915

• PubMed: 8901865 
• DOI: https://doi.org/10.1038/nsb1196-912
• Primary Citation Related Structures: 
  1LDG

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.92 kDa 
• Atom Count: 2,654 
• Modeled Residue Count: 315 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE	A	316	Plasmodium falciparum	Mutation(s): 0  EC: 1.1.1.27
UniProt
Find proteins for Q27743 (Plasmodium falciparum (isolate CDC / Honduras)) Explore Q27743  Go to UniProtKB:  Q27743

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
OXM	C [auth A]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OXM	BindingDB:  1LDG	IC50: min: 9.25e+4, max: 9.44e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.2	α = 90
b = 86.8	β = 90
c = 90.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-17 
Deposition Author(s): Dunn, C., Banfield, M., Barker, J., Higham, C., Moreton, K., Turgut-Balik, D., Brady, L., Holbrook, J.J.

Revision History  

• Version 1.0: 1997-09-17
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2013-11-06
  Changes: Non-polymer description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other