7WYF

Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with its inhibitor 50

• PDB DOI: https://doi.org/10.2210/pdb7WYF/pdb

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


• Deposited: 2022-02-16 Released: 2023-02-22 
• Deposition Author(s): Zhu, L., Li, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.359 
• R-Value Work: 0.258 
• R-Value Observed: 0.263 

Literature

Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with its inhibitor 50

Zhu, L., Li, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.86 kDa 
• Atom Count: 2,928 
• Modelled Residue Count: 361 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	431	Plasmodium falciparum	Mutation(s): 0  Gene Names: dhod EC: 1.3.5.2
UniProt
Find proteins for Q08210 (Plasmodium falciparum (isolate 3D7)) Explore Q08210  Go to UniProtKB:  Q08210

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
7NE (Subject of Investigation/LOI)	D [auth A]	ethyl 2-(naphthalen-2-ylamino)-4-oxidanylidene-furan-3-carboxylate C17 H15 N O4 KDQAZKWASGPNFD-UHFFFAOYSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.359 
• R-Value Work: 0.258 
• R-Value Observed: 0.263 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.71	α = 90
b = 71.77	β = 90
c = 179.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Zhu, L., Li, H.

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Funding Organization	Location	Grant Number
Other government	China	81222046

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description