Research workbench
2.4 ångström crystal structure of dihydroorotase (pyrc) from campylobacter jejuni.
Analyse 2.4 ångström crystal structure of dihydroorotase (pyrc) from campylobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNU
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- Q0PBP6
- Ligands
- ZN, PO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 338 | 38% helix, 17% strand | Q0PBP6 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 334 | 35% helix, 18% strand | Q0PBP6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.58 | 0.85 | 18 | empty |
| 2 | 209 | 0.50 | 0.76 | 29 | empty |
| 3 | 101 | 0.47 | 0.80 | 25 | empty |
| 4 | 170 | 0.45 | 0.74 | 28 | empty |
| 5 | 98 | 0.38 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1045 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 3PNU · 2.4 Angstrom Crystal Structure of Dihydroorotase (pyrC) from Campylobacter jejuni. · 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 Q0PBP6
- Elsewhere: RCSB PDB 3PNU · PDBe 3PNU · UniProt Q0PBP6
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