MolNFT v1 · #124325 · protein
Crystal structure of tmribu, the riboflavin-binding S subunit from the thermotoga maritima ecf transporter
5KBW · Riboflavin transporter ribu: “Crystal structure of tmribu, the riboflavin-binding S subunit from the thermotoga maritima ecf transporter”. X-ray diffraction, 1 ligand (RBF), 4 pockets (best druggability 0.74). MolNFT v1 #124325 on…
- PDB
- 5KBW
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin transporter ribu
- UniProt
- Q9X1G6
- Ligands
- RBF
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin transporter ribu | protein | 170 | 82% helix, 2% strand | Q9X1G6 |
| B | Riboflavin transporter ribu | protein | 171 | 82% helix, 2% strand | Q9X1G6 |
Ligands and binding sites
- RBF · Riboflavin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.74 | 0.92 | 24 | RBF |
| 2 | 619 | 0.72 | 0.79 | 55 | empty |
| 3 | 189 | 0.71 | 0.88 | 26 | RBF |
| 4 | 102 | 0.40 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5KBW · Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1G6 · AlphaFold monomer V2.0 prediction for riboflavin transporter ribu (Q9X1G6) · 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 Q9X1G6
- Elsewhere: RCSB PDB 5KBW · PDBe 5KBW · UniProt Q9X1G6
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