5H2Z | pdb_00005h2z

Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with 7GF

• PDB DOI: https://doi.org/10.2210/pdb5H2Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli O103:H2 str. 12009
• Mutation(s): No 


• Deposited: 2016-10-19 Released: 2017-03-01 
• Deposition Author(s): Wu, D., Huang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with 7GF

Huang, J., Wu, D.

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: 43.92 kDa 
• Atom Count: 2,998 
• 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
7GF	H [auth A]	methyl (2Z)-3-azanyl-2-[3-(4-bromophenyl)-4-oxidanylidene-1,3-thiazolidin-2-ylidene]propanoate C13 H13 Br N2 O3 S UEDYOLMWFOHHRV-BENRWUELSA-N
ORO	C [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	F [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.875	α = 90
b = 90.875	β = 90
c = 123.17	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data processing
HKL-3000	data scaling
PHENIX	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Wu, D., Huang, J.

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description