Research workbench
Crystal structure of a bacterial homologue of sweet transporters
Analyse Crystal structure of a bacterial homologue of sweet transporters in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RNG
- Type
- protein
- Length
- 494 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MTN3/SALIVA family
- UniProt
- B5YGD6
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | MTN3/SALIVA family | protein | 82 | 84% helix, 0% strand | B5YGD6 |
| C, D | MTN3/SALIVA family | protein | 83 | 84% helix, 0% strand | B5YGD6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B, D, E, F
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.84 | 0.99 | 26 | empty |
| 2 | 178 | 0.83 | 0.97 | 27 | empty |
| 3 | 161 | 0.83 | 0.98 | 26 | empty |
| 4 | 284 | 0.82 | 0.92 | 34 | OLC |
| 5 | 397 | 0.75 | 0.84 | 48 | OLC |
Interfaces
9 interfaces between chains.
- B–D · 1745 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1720 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1717 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 761 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 577 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4RNG · Crystal structure of a bacterial homologue of SWEET transporters · 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 B5YGD6
- Elsewhere: RCSB PDB 4RNG · PDBe 4RNG · UniProt B5YGD6
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