MolNFT v1 · #115769 · protein
The 3.7 a resolution structure of a eukaryotic sweet transporter
5CTH · Bidirectional sugar transporter SWEET2B: “The 3.7 a resolution structure of a eukaryotic sweet transporter”. X-ray diffraction, 1 ligand (BNG), 9 pockets (best druggability 0.80). MolNFT v1 #115769 on GenesisL1: 3D structure…
- PDB
- 5CTH
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bidirectional sugar transporter SWEET2B
- UniProt
- Q5N8J1
- Ligands
- BNG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bidirectional sugar transporter SWEET2B | protein | 212 | 80% helix, 0% strand | Q5N8J1 |
| B | Bidirectional sugar transporter SWEET2B | protein | 215 | 82% helix, 0% strand | Q5N8J1 |
| C | Bidirectional sugar transporter SWEET2B | protein | 213 | 78% helix, 0% strand | Q5N8J1 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · chains A, B
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 5 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.80 | 0.84 | 54 | PE5 |
| 2 | 617 | 0.79 | 0.84 | 50 | PE5 |
| 3 | 566 | 0.78 | 0.84 | 52 | PE5 |
| 4 | 654 | 0.65 | 0.74 | 57 | MES, PE5 |
| 5 | 365 | 0.62 | 0.77 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 803 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 803 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- Q5N8J1 · AlphaFold monomer V2.0 prediction for bidirectional sugar transporter SWEET2B (Q5N8J1) · a predicted model of the same protein · chain B 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 Q5N8J1
- Elsewhere: RCSB PDB 5CTH · PDBe 5CTH · UniProt Q5N8J1
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