MolNFT v1 · #115768 · protein
The 3.1 a resolution structure of a eukaryotic sweet transporter
5CTG · Bidirectional sugar transporter SWEET2B: “The 3.1 a resolution structure of a eukaryotic sweet transporter”. X-ray diffraction, 1 ligand (BNG), 9 pockets (best druggability 0.81). MolNFT v1 #115768 on GenesisL1: 3D structure…
- PDB
- 5CTG
- Type
- protein
- Length
- 649 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 0.81
Structure
x-ray diffraction · 3 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bidirectional sugar transporter SWEET2B | protein | 214 | 83% helix, 0% strand | Q5N8J1 |
| B | Bidirectional sugar transporter SWEET2B | protein | 220 | 79% helix, 0% strand | Q5N8J1 |
| C | Bidirectional sugar transporter SWEET2B | protein | 215 | 83% helix, 0% strand | Q5N8J1 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, C, B
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · 2 copies · chains A, B
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 | 687 | 0.81 | 0.85 | 49 | empty |
| 2 | 667 | 0.80 | 0.84 | 52 | PE5 |
| 3 | 520 | 0.78 | 0.85 | 48 | PE5 |
| 4 | 361 | 0.62 | 0.77 | 40 | empty |
| 5 | 329 | 0.59 | 0.76 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 886 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 833 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CTG · The 3.1 A resolution structure of a eukaryotic SWEET transporter · the same entry in another collection · chain A against A, TM-score 1.00
- Q5N8J1 · AlphaFold monomer V2.0 prediction for bidirectional sugar transporter SWEET2B (Q5N8J1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5CTG · PDBe 5CTG · UniProt Q5N8J1
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