Research workbench
Crystal structure of dihydroorotase in complex with malate at PH9 from saccharomyces cerevisiae
Analyse Crystal structure of dihydroorotase in complex with malate at PH9 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L0K
- Type
- protein
- Length
- 1,455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- P20051
- Ligands
- LMR, ZN
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dihydroorotase (EC 3.5.2.3) | protein | 364 | 35% helix, 18% strand | P20051 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 363 | 35% helix, 17% strand | P20051 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic 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
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.78 | 0.81 | 78 | empty |
| 2 | 926 | 0.78 | 0.81 | 82 | empty |
| 3 | 313 | 0.62 | 0.79 | 30 | empty |
| 4 | 354 | 0.59 | 0.76 | 40 | empty |
| 5 | 134 | 0.50 | 0.79 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1188 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1161 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 422 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 211 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6L0K · Crystal structure of dihydroorotase in complex with malate at pH9 from Saccharomyces… · 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 B 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 6L0K · PDBe 6L0K · UniProt P20051
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