Research workbench
Crystal structure of dihydroorotase in complex with plumbagin from saccharomyces cerevisiae
Analyse Crystal structure of dihydroorotase in complex with plumbagin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CA1
- Type
- protein
- Length
- 1,456 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, 90R, ZN
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Dihydroorotase (EC 3.5.2.3) | protein | 364 | 32% helix, 17% strand | P20051 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 2 copies · chains A, B
- 90R · 5-hydroxy-2-methylnaphthalene-1,4-dione · ligand · 2 copies · chains C, D
- ZN · Zinc ion · metal · 8 copies · chains A, C, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.79 | 0.81 | 77 | empty |
| 2 | 622 | 0.74 | 0.81 | 47 | empty |
| 3 | 699 | 0.67 | 0.75 | 48 | empty |
| 4 | 461 | 0.63 | 0.76 | 35 | empty |
| 5 | 393 | 0.62 | 0.77 | 43 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1194 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1188 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 524 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 431 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 220 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 7CA1 · Crystal structure of dihydroorotase in complex with plumbagin 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 7CA1 · PDBe 7CA1 · UniProt P20051
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