Research workbench
Lumazine synthase RIBH1 from brucella melitensis (gene BMEI1187, swiss-prot entry Q8YGH2) complexed with inhibitor 5-nitro-6-(D- ribitylamino)-2,4(1H,3H) pyrimidinedione
Analyse Lumazine synthase RIBH1 from brucella melitensis (gene BMEI1187, swiss-prot… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O6H
- Type
- protein
- Length
- 734 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
- Q8YGH2
- Ligands
- INI, CA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 147 | 53% helix, 22% strand | Q8YGH2 |
| C | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 146 | 53% helix, 21% strand | Q8YGH2 |
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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.78 | 0.82 | 64 | empty |
| 2 | 226 | 0.71 | 0.87 | 32 | INI |
| 3 | 220 | 0.71 | 0.87 | 33 | INI |
| 4 | 228 | 0.70 | 0.86 | 31 | INI |
| 5 | 220 | 0.70 | 0.86 | 32 | INI |
Interfaces
5 interfaces between chains.
- B–C · 1293 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1274 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1274 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1268 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1228 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2O6H · Lumazine synthase RibH1 from Brucella melitensis (Gene BMEI1187, Swiss-Prot entry Q8YGH2)… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8YGH2 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase 1 (Q8YGH2) · 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 Q8YGH2
- Elsewhere: RCSB PDB 2O6H · PDBe 2O6H · UniProt Q8YGH2
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