Research workbench
Crystal structure of lumazine synthase from brucella abortus
Analyse Crystal structure of lumazine synthase from brucella abortus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DI0
- Type
- protein
- Length
- 735 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lumazine synthase
- UniProt
- P61711
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lumazine synthase | protein | 148 | 55% helix, 21% strand | P61711 |
| C | Lumazine synthase | protein | 146 | 55% helix, 21% strand | P61711 |
| D | Lumazine synthase | protein | 147 | 54% helix, 21% strand | P61711 |
| E | Lumazine synthase | protein | 146 | 55% helix, 20% strand | P61711 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 13 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.78 | 0.88 | 31 | PO4 |
| 2 | 364 | 0.78 | 0.87 | 35 | PO4 |
| 3 | 966 | 0.77 | 0.79 | 61 | empty |
| 4 | 359 | 0.77 | 0.87 | 34 | PO4 |
| 5 | 368 | 0.76 | 0.86 | 37 | PO4 |
Interfaces
5 interfaces between chains.
- A–B · 1347 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1346 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1344 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1340 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1340 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1DI0 · Crystal structure of lumazine synthase from brucella abortus · the same entry in another collection · chain E against E, TM-score 1.00
- P61711 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase 2 (P61711) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P61711
- Elsewhere: RCSB PDB 1DI0 · PDBe 1DI0 · UniProt P61711
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