MolNFT v1 · #171123 · protein
Crystal structure of mhst in complex with L-valine
6YU5 · Sodium-dependent transporter: “Crystal structure of mhst in complex with L-valine”. X-ray diffraction, 3 ligands (BNG, VAL, NA), 11 pockets (best druggability 0.64). MolNFT v1 #171123 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YU5
- Type
- protein
- Length
- 886 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent transporter
- UniProt
- A0A4Y7X244
- Ligands
- BNG, VAL, NA
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent transporter | protein | 441 | 75% helix, 0% strand | A0A4Y7X244 |
| B | Sodium-dependent transporter | protein | 445 | 75% helix, 0% strand | A0A4Y7X244 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 20 copies · chains A, B
- VAL · Valine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.64 | 0.83 | 40 | empty |
| 2 | 163 | 0.62 | 0.84 | 29 | empty |
| 3 | 139 | 0.45 | 0.77 | 16 | empty |
| 4 | 112 | 0.45 | 0.78 | 18 | LMT |
| 5 | 139 | 0.44 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 335 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6YU5 · Crystal structure of MhsT in complex with L-valine · 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 A0A4Y7X244
- Elsewhere: RCSB PDB 6YU5 · PDBe 6YU5 · UniProt A0A4Y7X244
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