MolNFT v1 · #121833 · protein
X-ray structure of the TS3 human serotonin transporter complexed with S-citalopram at the central site
5I71 · Sodium-dependent serotonin transporter: “X-ray structure of the TS3 human serotonin transporter complexed with S-citalopram at the central site”. X-ray diffraction, 5 ligands (68P, CLR, D12), 14 pockets (best druggability 0.84).…
- PDB
- 5I71
- Type
- protein
- Length
- 974 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
- 68P, CLR, D12, NAG, NA
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 542 | 65% helix, 1% strand | P31645 |
| B | 8B6 antibody, heavy chain | protein | 218 | 1% helix, 51% strand | — |
| C | 8B6 antibody, light chain | protein | 214 | 6% helix, 48% strand | — |
Ligands and binding sites
- 68P · (1S)-1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- D12 · Dodecane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- HEX · Hexane · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.84 | 0.86 | 73 | 68P, D12 |
| 2 | 57 | 0.72 | 0.98 | 23 | empty |
| 3 | 53 | 0.68 | 0.96 | 18 | empty |
| 4 | 722 | 0.65 | 0.74 | 61 | empty |
| 5 | 361 | 0.60 | 0.77 | 35 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1867 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5I71 · X-ray structure of the ts3 human serotonin transporter complexed with s-citalopram 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 5I71 · PDBe 5I71 · UniProt P31645
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