3W7R | pdb_00003w7r

Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097

• PDB DOI: https://doi.org/10.2210/pdb3W7R/pdb

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


• Deposited: 2013-03-06 Released: 2014-03-12 
• Deposition Author(s): Inaoka, D.K., Iida, M., Tabuchi, T., Lee, N., Hashimoto, S., Matsuoka, S., Kuranaga, T., Shiba, T., Sakamoto, K., Suzuki, S., Balogun, E.O., Nara, T., Aoki, T., Inoue, M., Honma, T., Tanaka, A., Harada, S., Kita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.172 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097

Inaoka, D.K., Iida, M., Tabuchi, T., Lee, N., Hashimoto, S., Matsuoka, S., Kuranaga, T., Shiba, T., Sakamoto, K., Suzuki, S., Balogun, E.O., Nara, T., Aoki, T., Inoue, M., Honma, T., Tanaka, A., Harada, S., Kita, K.

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: 47.65 kDa 
• Atom Count: 3,626 
• Modeled Residue Count: 367 
• 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: PyrD 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	J [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
W7A	I [auth A]	2,6-dioxo-5-[2-(4-phenylphenyl)ethyl]-1,2,3,6- tetrahydropyrimidine-4-carboxylic acid C19 H16 N2 O4 UYFCRZJXNNSAAC-UHFFFAOYSA-N
DDQ	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C12 H27 N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N
ORO	GA [auth A]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
SO4	HA [auth A], IA [auth A], JA [auth A], KA [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.172 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.449	α = 90
b = 90.449	β = 90
c = 123.063	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Inaoka, D.K., Iida, M., Tabuchi, T., Lee, N., Hashimoto, S., Matsuoka, S., Kuranaga, T., Shiba, T., Sakamoto, K., Suzuki, S., Balogun, E.O., Nara, T., Aoki, T., Inoue, M., Honma, T., Tanaka, A., Harada, S., Kita, K.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description