MolNFT v1 · #155211 · protein
Crystal structure of dihydroorotase in complex with malate at PH7 from saccharomyces cerevisiae
6L0A: “Crystal structure of dihydroorotase in complex with malate at PH7 from saccharomyces cerevisiae”. X-ray diffraction, 2 ligands (LMR, ZN), 20 pockets (best druggability 0.79). MolNFT v1 #155211 on GenesisL1: 3D structure, binding…
- PDB
- 6L0A
- Type
- protein
- Length
- 1,454 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 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Dihydroorotase (EC 3.5.2.3) | protein | 363 | 37% helix, 18% strand | P20051 |
| C | Dihydroorotase (EC 3.5.2.3) | protein | 365 | 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.79 | 0.83 | 72 | empty |
| 2 | 708 | 0.77 | 0.82 | 72 | empty |
| 3 | 216 | 0.58 | 0.80 | 30 | empty |
| 4 | 122 | 0.48 | 0.79 | 22 | empty |
| 5 | 143 | 0.44 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1179 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1157 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 452 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 421 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6L0A · Crystal structure of dihydroorotase in complex with malate at pH7 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 6L0A · PDBe 6L0A · UniProt P20051
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