Research workbench
Crystal structure of dihydroorotase in complex with 5-fluoroorotic acid from Saccharomyces cerevisiae
Analyse Crystal structure of dihydroorotase in complex with 5-fluoroorotic acid from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CA0
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- P20051
- Ligands
- FOT, ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.5 · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydroorotase (EC 3.5.2.3) | protein | 364 | 34% helix, 18% strand | P20051 |
Ligands and binding sites
- FOT · 5-fluoro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.79 | 0.82 | 81 | empty |
| 2 | 706 | 0.78 | 0.83 | 64 | empty |
| 3 | 239 | 0.60 | 0.80 | 33 | empty |
| 4 | 131 | 0.43 | 0.76 | 23 | empty |
| 5 | 89 | 0.42 | 0.79 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1175 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1157 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 424 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 208 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 7CA0 · Crystal structure of dihydroorotase in complex with 5-fluoroorotic acid from… · the same entry in another collection · chain A against A, TM-score 1.00
- P20051 · AlphaFold monomer V2.0 prediction for dihydroorotase (P20051) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P20051
- Elsewhere: RCSB PDB 7CA0 · PDBe 7CA0 · UniProt P20051
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