MolNFT v1 · #98657 · protein
Crystal structure of a dihydroorotase from burkholderia cenocepacia J2315
4LFY: “Crystal structure of a dihydroorotase from burkholderia cenocepacia J2315”. X-ray diffraction, 2 ligands (ZN, CA), 4 pockets (best druggability 0.58). MolNFT v1 #98657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4LFY
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotase
- EC
- 3.5.2.3
- UniProt
- B4EEU0
- Ligands
- ZN, CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotase (EC 3.5.2.3) | protein | 349 | 38% helix, 17% strand | B4EEU0 |
| B | Dihydroorotase (EC 3.5.2.3) | protein | 353 | 39% helix, 17% strand | B4EEU0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.58 | 0.77 | 35 | ZN |
| 2 | 293 | 0.57 | 0.77 | 36 | empty |
| 3 | 124 | 0.45 | 0.77 | 23 | empty |
| 4 | 95 | 0.43 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1196 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4LFY · Crystal structure of a dihydroorotase from Burkholderia cenocepacia J2315 · 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 B4EEU0
- Elsewhere: RCSB PDB 4LFY · PDBe 4LFY · UniProt B4EEU0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.