MolNFT v1 · #13021 · protein
Lumazine synthase from S.POMBE bound to riboflavin
1KYV · 6,7-dimethyl-8-ribityllumazine synthase: “Lumazine synthase from S.POMBE bound to riboflavin”. X-ray diffraction, 2 ligands (RBF, PO4), 9 pockets (best druggability 0.78). MolNFT v1 #13021 on GenesisL1: 3D structure, binding sites…
- PDB
- 1KYV
- Type
- protein
- Length
- 742 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
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 52% helix, 20% strand | Q9UUB1 |
| C | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 149 | 52% helix, 21% strand | Q9UUB1 |
| E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 152 | 51% helix, 19% 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
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.78 | 0.88 | 53 | empty |
| 2 | 299 | 0.76 | 0.88 | 38 | PO4, RBF |
| 3 | 327 | 0.70 | 0.83 | 33 | PO4, RBF |
| 4 | 298 | 0.69 | 0.84 | 32 | PO4, RBF |
| 5 | 291 | 0.68 | 0.83 | 35 | PO4, RBF |
Interfaces
10 interfaces between chains.
- A–E · 1349 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1170 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1169 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1160 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1154 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1KYV · Lumazine Synthase from S.pombe bound to riboflavin · the same entry in another collection · chain E against E, 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 1KYV · PDBe 1KYV · UniProt Q9UUB1
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