MolNFT v1 · #99911 · protein
Crystal structure of thit with small molecule bat-25
4MHW · Thiamine transporter thit: “Crystal structure of thit with small molecule bat-25”. X-ray diffraction, 2 ligands (BNG, 0YN), 4 pockets (best druggability 0.73). MolNFT v1 #99911 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4MHW
- Type
- protein
- Length
- 353 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine transporter thit
- UniProt
- D8KFM5
- Ligands
- BNG, 0YN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine transporter thit | protein | 177 | 75% helix, 3% strand | D8KFM5 |
| B | Thiamine transporter thit | protein | 176 | 74% helix, 3% strand | D8KFM5 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 3 copies · chains A, B
- 0YN · 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 16 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
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 | 195 | 0.73 | 0.89 | 30 | 0YN |
| 2 | 212 | 0.72 | 0.88 | 33 | 0YN, PG0 |
| 3 | 332 | 0.68 | 0.81 | 29 | P6G, PEG, PG4 |
| 4 | 106 | 0.37 | 0.73 | 18 | PEG |
Interfaces
1 interface between chains.
- A–B · 580 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MHW · Crystal structure of ThiT with small molecule BAT-25 · 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 D8KFM5
- Elsewhere: RCSB PDB 4MHW · PDBe 4MHW · UniProt D8KFM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.