MolNFT v1 · #16171 · protein
Crystal structure of lumazine synthase from aquifex aeolicus in complex with inhibitor: 3-(7-hydroxy-8-ribityllumazine-6-YL)PROPIONIC acid
1NQX · 6,7-dimethyl-8-ribityllumazine synthase: “Crystal structure of lumazine synthase from aquifex aeolicus in complex with inhibitor…”. X-ray diffraction, 2 ligands (RLP, PO4), 7 pockets (best druggability 0.74). MolNFT v1 #16171 on…
- PDB
- 1NQX
- 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
- RLP, PO4
- 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
- RLP · 3-(7-hydroxy-8-ribityllumazine-6-yl) propionic acid · 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
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 | 606 | 0.74 | 0.81 | 31 | empty |
| 2 | 302 | 0.69 | 0.83 | 34 | PO4, RLP |
| 3 | 288 | 0.69 | 0.84 | 38 | PO4, RLP |
| 4 | 298 | 0.68 | 0.83 | 36 | PO4, RLP |
| 5 | 304 | 0.68 | 0.82 | 36 | PO4, RLP |
Interfaces
5 interfaces between chains.
- A–B · 1541 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1541 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1535 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1531 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1NQX · 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 1NQX · PDBe 1NQX · UniProt O66529
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