Research workbench
Lumazine synthase from S.POMBE bound to nitropyrimidinedione
Analyse Lumazine synthase from S.POMBE bound to nitropyrimidinedione in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KYY
- Type
- protein
- Length
- 744 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
- INI, PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 149 | 52% helix, 21% strand | Q9UUB1 |
| B, D | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 52% helix, 21% strand | Q9UUB1 |
| C | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 149 | 54% helix, 21% strand | Q9UUB1 |
| E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 152 | 51% helix, 20% strand | Q9UUB1 |
Ligands and binding sites
- INI · 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.81 | 0.87 | 39 | empty |
| 2 | 297 | 0.74 | 0.87 | 40 | PO4, INI |
| 3 | 303 | 0.69 | 0.83 | 37 | PO4, INI |
| 4 | 289 | 0.69 | 0.83 | 32 | PO4, INI |
| 5 | 335 | 0.68 | 0.82 | 37 | PO4, INI |
Interfaces
10 interfaces between chains.
- A–E · 1332 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1180 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1176 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1169 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1167 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1KYY · Lumazine Synthase from S.pombe bound to nitropyrimidinedione · the same entry in another collection · chain D against D, 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 B 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 1KYY · PDBe 1KYY · UniProt Q9UUB1
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