6R8G | pdb_00006r8g

Crystal structure of malate dehydrogenase from Plasmodium Falciparum in complex with 4-(3,4-difluorophenyl)thiazol-2-amine

• PDB DOI: https://doi.org/10.2210/pdb6R8G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-01 Released: 2020-04-15 
• Deposition Author(s): Romero, A.R., Calderone, V., Gentili, M., Lunev, S., Groves, M., Popowicz, G., Domling, A., Sattler, M.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

A Fragment-Based Approach Identifies an Allosteric Pocket that Impacts Malate Dehydrogenase Activity

Romero, A.R., Lunev, S., Popowicz, G., Calderone, V., Gentili, M., Sattler, M., Plewka, J., Taube, M., Kozak, M., Holak, T.A., Domling, A., Groves, M.

(2021) Commun Biol 

• DOI: https://doi.org/10.1038/s42003-021-02442-1

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 (software)

Macromolecule Content 

• Total Structure Weight: 142.99 kDa 
• Atom Count: 9,848 
• Modeled Residue Count: 1,246 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D	324	Plasmodium falciparum	Mutation(s): 0  EC: 1.1.1.37
UniProt
Find proteins for Q6VVP7 (Plasmodium falciparum) Explore Q6VVP7  Go to UniProtKB:  Q6VVP7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
JUT	E [auth A], H [auth C], I [auth D], J [auth D]	4-[3,4-bis(fluoranyl)phenyl]-1,3-thiazol-2-amine C9 H6 F2 N2 S NDCSJUJQMRFHEX-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.76	α = 90
b = 106.89	β = 90
c = 145.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Romero, A.R., Calderone, V., Gentili, M., Lunev, S., Groves, M., Popowicz, G., Domling, A., Sattler, M.

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Funding Organization	Location	Grant Number
European Union	Netherlands	675555

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2021-08-04
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description