4LS2 | pdb_00004ls2

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A313

• PDB DOI: https://doi.org/10.2210/pdb4LS2/pdb

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


• Deposited: 2013-07-21 Released: 2014-07-23 
• Deposition Author(s): Zhu, L., Li, H., Ren, X., Zhu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A313

Zhu, L., Li, H., Ren, X., Zhu, J.

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: 44.14 kDa 
• Atom Count: 3,073 
• Modeled Residue Count: 364 
• 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
3XS	J [auth A]	2-[(E)-{2-[4-(3-methoxyphenyl)-1,3-thiazol-2-yl]hydrazinylidene}methyl]benzoic acid C18 H15 N3 O3 S CRNTYYFZANKWHU-VXLYETTFSA-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]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.39	α = 90
b = 90.39	β = 90
c = 122.9	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Zhu, L., Li, H., Ren, X., Zhu, J.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description