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Crystallographic structure of trimeric riboflavin synthase from brucella abortus in complex with roseoflavin
Analyse Crystallographic structure of trimeric riboflavin synthase from brucella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G6I
- Type
- protein
- Length
- 596 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin synthase subunit alpha
- EC
- 2.5.1.9
- UniProt
- G8SX20
- Ligands
- RS3
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin synthase subunit alpha (EC 2.5.1.9) | protein | 200 | 18% helix, 43% strand | G8SX20 |
| B | Riboflavin synthase subunit alpha (EC 2.5.1.9) | protein | 197 | 19% helix, 44% strand | G8SX20 |
| C | Riboflavin synthase subunit alpha (EC 2.5.1.9) | protein | 199 | 18% helix, 43% strand | G8SX20 |
Ligands and binding sites
- RS3 · 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol · ligand · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.81 | 0.87 | 59 | RS3 |
| 2 | 679 | 0.68 | 0.76 | 61 | RS3 |
| 3 | 89 | 0.39 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1737 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1077 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4G6I · Crystallographic structure of trimeric riboflavin synthase from Brucella abortus in… · the same entry in another collection · chain A against A, TM-score 1.00
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 G8SX20
- Elsewhere: RCSB PDB 4G6I · PDBe 4G6I · UniProt G8SX20
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