Research workbench
Structure of human SGLT2-MAP17 complex bound with empagliflozin
Analyse Structure of human SGLT2-MAP17 complex bound with empagliflozin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VSI
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM/GLUCOSE cotransporter 2; PDZK1-interacting protein 1
- UniProt
- P31639, Q13113
- Ligands
- PLM, 7R3
- Pockets
- 7 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM/GLUCOSE cotransporter 2 | protein | 586 | 73% helix, 1% strand | P31639 |
| B | PDZK1-interacting protein 1 | protein | 30 | 83% helix, 0% strand | Q13113 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A
- 7R3 · (2S,3R,4R,5S,6R)-2-[4-chloranyl-3-[[4-[(3S)-oxolan-3-yl]oxyphenyl]methyl]phenyl]-6-(hydroxymethyl)oxane-3, 4,5-triol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.81 | 0.82 | 95 | 7R3 |
| 2 | 332 | 0.54 | 0.74 | 41 | empty |
| 3 | 160 | 0.51 | 0.79 | 18 | empty |
| 4 | 146 | 0.47 | 0.76 | 21 | empty |
| 5 | 75 | 0.41 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 450 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 lipid (disulfide, palmitoylation).
Compared structures
- 7VSI · Structure of human SGLT2-MAP17 complex bound with empagliflozin · the same entry in another collection · chain A against A, TM-score 1.00
- P31639 · AlphaFold monomer V2.0 prediction for SODIUM/GLUCOSE cotransporter 2 (P31639) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q13113 · AlphaFold monomer V2.0 prediction for PDZK1-interacting protein 1 (Q13113) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 P31639
- Every structure of UniProt Q13113
- Elsewhere: RCSB PDB 7VSI · PDBe 7VSI · UniProt P31639 · UniProt Q13113
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