MolNFT v1 · #155218 · protein
Crystal structure of dihydroorotase in complex with malate at PH7.5 from saccharomyces cerevisiae
6L0J: “Crystal structure of dihydroorotase in complex with malate at PH7.5 from saccharomyces cerevisiae”. X-ray diffraction, 2 ligands (LMR, ZN), 18 pockets (best druggability 0.73). MolNFT v1 #155218 on GenesisL1: 3D structure, binding…
- PDB
- 6L0J
- 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
- 18 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydroorotase (EC 3.5.2.3) | protein | 363 | 36% helix, 18% strand | P20051 |
| D, B | Dihydroorotase (EC 3.5.2.3) | protein | 364 | 37% helix, 18% strand | P20051 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.73 | 0.79 | 63 | empty |
| 2 | 139 | 0.41 | 0.75 | 22 | empty |
| 3 | 154 | 0.41 | 0.74 | 34 | empty |
| 4 | 114 | 0.40 | 0.76 | 22 | empty |
| 5 | 122 | 0.39 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- D–B · 1197 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1159 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 445 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6L0J · Crystal structure of Dihydroorotase in complex with malate at pH7.5 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 6L0J · PDBe 6L0J · UniProt P20051
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