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Crystal structure of a dihydroorotase
Analyse Crystal structure of a dihydroorotase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGJ
- Type
- protein
- Length
- 2,160 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- UniProt
- Q8UAV1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase | protein | 379 | 24% helix, 28% strand | Q8UAV1 |
| B | Dihydroorotase | protein | 369 | 26% helix, 31% strand | Q8UAV1 |
| C | Dihydroorotase | protein | 317 | 27% helix, 21% strand | Q8UAV1 |
| D | Dihydroorotase | protein | 364 | 24% helix, 27% strand | Q8UAV1 |
| E | Dihydroorotase | protein | 372 | 26% helix, 27% strand | Q8UAV1 |
| F | Dihydroorotase | protein | 359 | 27% helix, 26% strand | Q8UAV1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- IMD · Imidazole · additive · 2 copies · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.68 | 0.83 | 36 | empty |
| 2 | 215 | 0.63 | 0.83 | 39 | empty |
| 3 | 387 | 0.61 | 0.77 | 62 | ZN |
| 4 | 244 | 0.60 | 0.80 | 38 | ZN |
| 5 | 205 | 0.59 | 0.81 | 44 | ZN, IMD |
Interfaces
9 interfaces between chains.
- E–F · 1096 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1093 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1079 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 600 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 581 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 modified (engineered, carboxylation).
Compared structures
- 2OGJ · Crystal structure of a dihydroorotase · the same entry in another collection · 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 Q8UAV1
- Elsewhere: RCSB PDB 2OGJ · PDBe 2OGJ · UniProt Q8UAV1
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