4ZMG

Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with DH03A338

• PDB DOI: https://doi.org/10.2210/pdb4ZMG/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-05-04 Released: 2016-05-04 
• Deposition Author(s): Ren, X.L., Zhu, J.S., Zhu, L.L., Li, H.L.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with DH03A338

Ren, X.L., Zhu, J.S., Zhu, L.L., Li, H.L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 43.86 kDa 
• Atom Count: 3,037 
• Modelled Residue Count: 365 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone), mitochondrial	A	390	Homo sapiens	Mutation(s): 0  Gene Names: DHODH EC: 1.3.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens) Explore Q02127  Go to UniProtKB:  Q02127
PHAROS:  Q02127 GTEx:  ENSG00000102967

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
4R5	D [auth A]	1-(3,5-difluoro-3'-methoxybiphenyl-4-yl)-3-(1,3-thiazol-5-yl)urea C17 H13 F2 N3 O2 S FLPJNPHNEKGCBD-UHFFFAOYSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.02	α = 90
b = 91.02	β = 90
c = 122.79	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Ren, X.L., Zhu, J.S., Zhu, L.L., Li, H.L.

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Funding Organization	Location	Grant Number
National Institutes of Health	China	81302697

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description