Research workbench
Crystal structure of lumazine synthase from aquifex aeolicus in complex with inhibitor: 5-(6-D-ribitylamino-2,4(1H,3H) pyrimidinedione-5-yl)-1-pentyl-phosphonic acid
Analyse Crystal structure of lumazine synthase from aquifex aeolicus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NQW
- Type
- protein
- Length
- 770 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
- O66529
- Ligands
- 5YL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 24% 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 | 154 | 50% helix, 24% strand | O66529 |
Ligands and binding sites
- 5YL · 5-(6-D-ribitylamino-2,4(1h,3h)pyrimidinedione-5-yl) pentyl-1-phosphonic acid · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.74 | 0.81 | 31 | empty |
| 2 | 295 | 0.68 | 0.83 | 35 | 5YL |
| 3 | 273 | 0.67 | 0.83 | 36 | 5YL |
| 4 | 293 | 0.67 | 0.82 | 36 | 5YL |
| 5 | 307 | 0.66 | 0.81 | 35 | 5YL |
Interfaces
10 interfaces between chains.
- D–E · 1568 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1563 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1558 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1555 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1552 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1NQW · Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- O66529 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (O66529) · 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 O66529
- Elsewhere: RCSB PDB 1NQW · PDBe 1NQW · UniProt O66529
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