MolNFT v1 · #121836 · protein
X-ray structure of the TS3 human serotonin transporter complexed with br-citalopram at the central site
5I74 · Sodium-dependent serotonin transporter: “X-ray structure of the TS3 human serotonin transporter complexed with br-citalopram at the central site”. X-ray diffraction, 4 ligands (69D, CLR, D12), 15 pockets (best druggability 0.84).…
- PDB
- 5I74
- 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
- 69D, CLR, D12, NAG
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 542 | 70% helix, 2% strand | P31645 |
| B | 8B6 antibody, heavy chain | protein | 218 | 4% helix, 52% strand | — |
| C | 8B6 antibody, light chain | protein | 214 | 6% helix, 46% strand | — |
Ligands and binding sites
- 69D · (1S)-1-(4-bromophenyl)-1-[3-(dimethylamino)propyl]-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
- HEX · Hexane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.84 | 0.86 | 80 | 69D, D12 |
| 2 | 55 | 0.73 | 0.99 | 22 | empty |
| 3 | 302 | 0.63 | 0.80 | 38 | empty |
| 4 | 513 | 0.61 | 0.75 | 50 | empty |
| 5 | 103 | 0.50 | 0.82 | 25 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1843 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5I74 · X-ray structure of the ts3 human serotonin transporter complexed with Br-citalopram at… · 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 5I74 · PDBe 5I74 · UniProt P31645
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