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The crystal structure of the ligand-free dihydroorotase from E. COLI

Analyse The crystal structure of the ligand-free dihydroorotase from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EG6
Type: protein
Length: 680 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydroorotase
EC: 3.5.2.3
UniProt: P05020
Ligands: ZN
Pockets: 10 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydroorotase (EC 3.5.2.3)	protein	343	38% helix, 17% strand	P05020
B	Dihydroorotase (EC 3.5.2.3)	protein	337	39% helix, 18% strand	P05020

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.63	0.79	37	ZN
2	333	0.59	0.77	39	empty
3	119	0.48	0.79	23	empty
4	127	0.47	0.78	22	empty
5	112	0.41	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1146 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

2EG6 · The crystal structure of the ligand-free dihydroorotase from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
P05020 · AlphaFold monomer V2.0 prediction for dihydroorotase (P05020) · a predicted model of the same protein · chain B 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 P05020
Elsewhere: RCSB PDB 2EG6 · PDBe 2EG6 · UniProt P05020

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