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Dihydroorotate dehydrogenase

Analyse Dihydroorotate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B4G
Type: protein
Length: 1,250 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydroorotate dehydrogenase
EC: 1.3.99.11
UniProt: Q57U83
Ligands: FMN, ORO, BR
Pockets: 14 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Dihydroorotate dehydrogenase (EC 1.3.99.11)	protein	312	39% helix, 23% strand	Q57U83
B, C	Dihydroorotate dehydrogenase (EC 1.3.99.11)	protein	313	40% helix, 23% strand	Q57U83

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
ORO · Orotic acid · ligand · 4 copies · chains A, B, C, D
BR · Bromide ion · ion · 11 copies · chains A, B, D, C
GOL · Glycerol · additive · 4 copies · chains A, B, D, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.88	0.90	157	FMN, ORO, BR
2	280	0.78	0.90	49	FMN, ORO
3	290	0.78	0.90	48	BR, FMN, ORO
4	122	0.62	0.86	21	empty
5	107	0.56	0.84	19	empty

Interfaces

5 interfaces between chains.

C–D · 2369 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2353 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 372 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 257 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 237 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2B4G · dihydroorotate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
Q57U83 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (fumarate) (Q57U83) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q57U83
Elsewhere: RCSB PDB 2B4G · PDBe 2B4G · UniProt Q57U83

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