MolNFT v1 · #121829 · protein
X-ray structure of the TS3 human serotonin transporter complexed with paroxetine at the central site
5I6X · Sodium-dependent serotonin transporter: “X-ray structure of the TS3 human serotonin transporter complexed with paroxetine at the central site”. X-ray diffraction, 5 ligands (CLR, 8PR, NAG), 14 pockets (best druggability 0.83).…
- PDB
- 5I6X
- Type
- protein
- Length
- 976 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent serotonin transporter; 8B6 antibody, heavy chain; 8B6 antibody, light…
- UniProt
- P31645
- Ligands
- CLR, 8PR, NAG, NA, CL
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 544 | 69% helix, 1% strand | P31645 |
| B | 8B6 antibody, heavy chain | protein | 218 | 3% helix, 50% strand | — |
| C | 8B6 antibody, light chain | protein | 214 | 6% helix, 46% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- 8PR · Paroxetine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.83 | 0.84 | 73 | LMT, 8PR |
| 2 | 730 | 0.66 | 0.74 | 66 | empty |
| 3 | 393 | 0.61 | 0.77 | 44 | empty |
| 4 | 67 | 0.51 | 0.86 | 23 | empty |
| 5 | 282 | 0.50 | 0.74 | 43 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1868 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 131 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5I6X · X-ray structure of the ts3 human serotonin transporter complexed with paroxetine at the… · 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 0.99
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 5I6X · PDBe 5I6X · UniProt P31645
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