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Crystal structure of dihydroorotase in complex with malate at PH6.5 from saccharomyces cerevisiae
Analyse Crystal structure of dihydroorotase in complex with malate at PH6.5 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L0I
- 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
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Dihydroorotase (EC 3.5.2.3) | protein | 364 | 35% helix, 17% strand | P20051 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 363 | 37% helix, 18% 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
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.78 | 0.83 | 75 | empty |
| 2 | 648 | 0.77 | 0.82 | 62 | empty |
| 3 | 230 | 0.61 | 0.81 | 27 | empty |
| 4 | 154 | 0.52 | 0.79 | 22 | empty |
| 5 | 69 | 0.42 | 0.81 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1189 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 404 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 211 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6L0I · Crystal structure of dihydroorotase in complex with malate at pH6.5 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 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 6L0I · PDBe 6L0I · UniProt P20051
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