Research workbench
Crystal structure of SODIUM/SUGAR symporter with bound galactose from vibrio parahaemolyticus
Analyse Crystal structure of SODIUM/SUGAR symporter with bound galactose from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DH4
- Type
- protein
- Length
- 2,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/GLUCOSE cotransporter
- UniProt
- P96169
- Ligands
- GAL, ER3, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | SODIUM/GLUCOSE cotransporter | protein | 512 | 75% helix, 0% strand | P96169 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- ER3 · Erbium (III) ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.88 | 0.88 | 56 | empty |
| 2 | 1045 | 0.87 | 0.87 | 64 | empty |
| 3 | 859 | 0.82 | 0.84 | 108 | GAL, NA |
| 4 | 862 | 0.81 | 0.83 | 107 | GAL, NA |
| 5 | 798 | 0.81 | 0.84 | 96 | GAL, NA |
Interfaces
4 interfaces between chains.
- A–B · 1543 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1542 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 271 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DH4 · Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- P96169 · AlphaFold monomer V2.0 prediction for SODIUM/GLUCOSE cotransporter (P96169) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P96169
- Elsewhere: RCSB PDB 3DH4 · PDBe 3DH4 · UniProt P96169
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