MolNFT v1 · #68544 · protein
1.8 ångström resolution crystal structure of dihydroorotase (pyrc) from salmonella enterica subsp. enterica serovar typhimurium str. LT2
3JZE: “1.8 ångström resolution crystal structure of dihydroorotase (pyrc) from salmonella enterica subsp. enterica…”. X-ray diffraction, 2 ligands (ZN, CL), 20 pockets (best druggability 0.63). MolNFT v1 #68544 on GenesisL1: 3D structure…
- PDB
- 3JZE
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- P06204
- Ligands
- ZN, CL
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydroorotase (EC 3.5.2.3) | protein | 344 | 38% helix, 18% strand | P06204 |
| B, D | Dihydroorotase (EC 3.5.2.3) | protein | 342 | 38% helix, 18% strand | P06204 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 8 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 6 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, 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 | 438 | 0.63 | 0.77 | 50 | empty |
| 2 | 304 | 0.56 | 0.76 | 37 | ZN, ACY |
| 3 | 266 | 0.55 | 0.77 | 26 | ACY |
| 4 | 152 | 0.53 | 0.80 | 26 | empty |
| 5 | 135 | 0.50 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1238 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1234 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 292 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 modified (additive adduct, carboxylation).
Compared structures
- 3JZE · 1.8 Angstrom resolution crystal structure of dihydroorotase (pyrC) from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- P06204 · AlphaFold monomer V2.0 prediction for dihydroorotase (P06204) · a predicted model of the same protein · 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 P06204
- Elsewhere: RCSB PDB 3JZE · PDBe 3JZE · UniProt P06204
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.