4RKA

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A347

• PDB DOI: https://doi.org/10.2210/pdb4RKA/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-12 Released: 2015-11-11 
• Deposition Author(s): Zhu, L., Ren, X., Zhu, J., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.228 
• R-Value Work: 0.163 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A347

Zhu, L., Ren, X., Zhu, J., Li, H.

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: 44.2 kDa 
• Atom Count: 2,997 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
3RY	J [auth A]	2-{[5-(naphthalen-1-ylmethyl)-4-oxo-4H-1lambda~4~,3-thiazol-2-yl]amino}benzoic acid C21 H16 N2 O3 S LOJPZHDHFDLIRT-UHFFFAOYSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.228 
• R-Value Work: 0.163 
• R-Value Observed: 0.167 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.65	α = 90
b = 90.65	β = 90
c = 122.45	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
auto	model building
REFMAC	refinement
HKL-2000	data reduction
iMOSFLM	data reduction
auto	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Zhu, L., Ren, X., Zhu, J., Li, H.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description