MolNFT v1 · #99815 · protein
Crystal structure of thit complexed with LMG116
4MES · Thiamine transporter thit: “Crystal structure of thit complexed with LMG116”. X-ray diffraction, 2 ligands (BNG, 26G), 5 pockets (best druggability 0.77). MolNFT v1 #99815 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4MES
- 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, 26G
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine transporter thit | protein | 176 | 74% helix, 3% strand | D8KFM5 |
| B | Thiamine transporter thit | protein | 177 | 73% helix, 3% strand | D8KFM5 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 7 copies · chains A, B
- 26G · 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 11 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 7 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.77 | 0.90 | 33 | 26G, PG4 |
| 2 | 237 | 0.75 | 0.89 | 31 | 26G, PG4 |
| 3 | 308 | 0.67 | 0.82 | 30 | PG4, P6G, PEG |
| 4 | 105 | 0.46 | 0.78 | 16 | BNG, PEG |
| 5 | 102 | 0.37 | 0.73 | 15 | PG4, PEG |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4MES · Crystal structure of ThiT complexed with LMG116 · the same entry in another collection · chain B against B, 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 4MES · PDBe 4MES · UniProt D8KFM5
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