MolNFT v1 · #35602 · protein
The crystal structure of E. COLI dihydroorotase complexed with 5- fluoroorotic acid
2EG8: “The crystal structure of E. COLI dihydroorotase complexed with 5- fluoroorotic acid”. X-ray diffraction, 2 ligands (FOT, ZN), 10 pockets (best druggability 0.60). MolNFT v1 #35602 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2EG8
- Type
- protein
- Length
- 679 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
- FOT, ZN
- Pockets
- 10 · best druggability 0.60
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 | 336 | 39% helix, 18% strand | P05020 |
Ligands and binding sites
- FOT · 5-fluoro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.60 | 0.79 | 31 | ZN, FOT |
| 2 | 320 | 0.58 | 0.77 | 36 | ZN, FOT |
| 3 | 136 | 0.52 | 0.80 | 22 | empty |
| 4 | 126 | 0.46 | 0.78 | 22 | empty |
| 5 | 95 | 0.39 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1139 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 2EG8 · The crystal structure of E. coli dihydroorotase complexed with 5-fluoroorotic acid · 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 2EG8 · PDBe 2EG8 · UniProt P05020
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