MolNFT v1 · #137179 · protein
Crystal structure of dihydroorotase pyrc from vibrio cholerae in complex with zinc at 1.95 a resolution.
5VGM: “Crystal structure of dihydroorotase pyrc from vibrio cholerae in complex with zinc at 1.95 a resolution.”. X-ray diffraction, 2 ligands (ZN, CL), 6 pockets (best druggability 0.63). MolNFT v1 #137179 on GenesisL1: 3D structure…
- PDB
- 5VGM
- Type
- protein
- Length
- 673 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- A0A0H6AFA4
- Ligands
- ZN, CL
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 331 | 40% helix, 20% strand | A0A0H6AFA4 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 342 | 38% helix, 20% strand | A0A0H6AFA4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.63 | 0.78 | 37 | empty |
| 2 | 290 | 0.57 | 0.77 | 40 | ACT |
| 3 | 50 | 0.36 | 0.79 | 14 | empty |
| 4 | 63 | 0.34 | 0.77 | 19 | ACT |
| 5 | 63 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1171 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation, carboxylation).
Compared structures
- 5VGM · Crystal structure of dihydroorotase pyrC from Vibrio cholerae in complex with zinc at… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0H6AFA4
- Elsewhere: RCSB PDB 5VGM · PDBe 5VGM · UniProt A0A0H6AFA4
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