MolNFT v1 · #36424 · protein
Lumazine synthase RIBH1 from brucella abortus (gene BRUAB1_0785, swiss-prot entry Q57DY1) complexed with inhibitor 5-nitro-6-(D- ribitylamino)-2,4(1H,3H) pyrimidinedione
2F59 · 6,7-dimethyl-8-ribityllumazine synthase 1: “Lumazine synthase RIBH1 from brucella abortus (gene BRUAB1_0785, swiss-prot entry Q57DY1) complexed with…”. X-ray diffraction, 2 ligands (INI, CA), 8 pockets (best druggability 0.78).…
- PDB
- 2F59
- Type
- protein
- Length
- 731 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase 1
- EC
- 2.5.1.78
- UniProt
- Q57DY1
- Ligands
- INI, CA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 146 | 53% helix, 21% strand | Q57DY1 |
| D | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 147 | 54% helix, 21% strand | Q57DY1 |
Ligands and binding sites
- INI · 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 5 copies · chains A, E, B, C, D
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.78 | 0.85 | 37 | empty |
| 2 | 210 | 0.70 | 0.86 | 31 | INI |
| 3 | 201 | 0.68 | 0.86 | 30 | INI |
| 4 | 179 | 0.68 | 0.86 | 24 | INI |
| 5 | 177 | 0.66 | 0.85 | 27 | INI |
Interfaces
7 interfaces between chains.
- A–E · 1303 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1303 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1303 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1273 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1270 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2F59 · Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1)… · the same entry in another collection · chain E against E, TM-score 1.00
- Q57DY1 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase 1 (Q57DY1) · a predicted model of the same protein · chain D 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 Q57DY1
- Elsewhere: RCSB PDB 2F59 · PDBe 2F59 · UniProt Q57DY1
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