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1.8 ångström resolution crystal structure of dihydroorotase (pyrc) from salmonella enterica subsp. enterica serovar typhimurium str. LT2
Analyse 1.8 ångström resolution crystal structure of dihydroorotase (pyrc) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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
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