Research workbench
Cryo-EM structure of the wild-type human serotonin transporter complexed with vilazodone, imipramine and 15B8 Fab
Analyse Cryo-EM structure of the wild-type human serotonin transporter complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LWD
- Type
- protein
- Length
- 769 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent serotonin transporter; Heavy chain antibody fragment; Light chain…
- UniProt
- P31645
- Ligands
- IXX, YG7, NAG
- Pockets
- 7 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 541 | 63% helix, 1% strand | P31645 |
| H | Heavy chain antibody fragment | protein | 118 | 11% helix, 31% strand | — |
| L | Light chain antibody fragment | protein | 110 | 0% helix, 37% strand | — |
Ligands and binding sites
- IXX · 3-(5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine · ligand · chains A
- YG7 · 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.80 | 0.83 | 67 | IXX, YG7 |
| 2 | 433 | 0.65 | 0.78 | 44 | empty |
| 3 | 180 | 0.47 | 0.76 | 31 | empty |
| 4 | 120 | 0.41 | 0.76 | 18 | empty |
| 5 | 65 | 0.35 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 883 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 567 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 262 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7LWD · Cryo-EM structure of the wild-type human serotonin transporter complexed with vilazodone… · the same entry in another collection · chain A against A, TM-score 1.00
- P31645 · AlphaFold monomer V2.0 prediction for sodium-dependent serotonin transporter (P31645) · 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 P31645
- Elsewhere: RCSB PDB 7LWD · PDBe 7LWD · UniProt P31645
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