Research workbench
Structure of 6,7-dimethyl-8-ribityllumazine synthase from schizosaccharomyces pombe mutant W27Y with bound riboflavin
Analyse Structure of 6,7-dimethyl-8-ribityllumazine synthase from schizosaccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A58
- Type
- protein
- Length
- 730 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase
- EC
- 2.5.1.78
- UniProt
- Q9UUB1
- Ligands
- RBF, PO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 146 | 53% helix, 20% strand | Q9UUB1 |
Ligands and binding sites
- RBF · Riboflavin · ligand · 5 copies · chains A, E, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.77 | 0.87 | 54 | empty |
| 2 | 345 | 0.70 | 0.82 | 32 | PO4, RBF |
| 3 | 352 | 0.69 | 0.82 | 32 | PO4, RBF |
| 4 | 353 | 0.69 | 0.82 | 35 | PO4, RBF |
| 5 | 331 | 0.69 | 0.82 | 33 | PO4, RBF |
Interfaces
10 interfaces between chains.
- A–E · 1162 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1157 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1148 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1148 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2A58 · Structure of 6,7-Dimethyl-8-ribityllumazine synthase from Schizosaccharomyces pombe… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UUB1 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (Q9UUB1) · a predicted model of the same protein · chain A 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 Q9UUB1
- Elsewhere: RCSB PDB 2A58 · PDBe 2A58 · UniProt Q9UUB1
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