MolNFT v1 · #121831 · protein
X-ray structure of the TS2 human serotonin transporter
5I6Z · Sodium-dependent serotonin transporter: “X-ray structure of the TS2 human serotonin transporter”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.83). MolNFT v1 #121831 on GenesisL1: 3D structure, binding sites…
- PDB
- 5I6Z
- 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
- NAG
- Pockets
- 12 · best druggability 0.83
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 | 544 | 70% helix, 2% strand | P31645 |
| B | 8B6 antibody, heavy chain | protein | 218 | 4% helix, 52% strand | — |
| C | 8B6 antibody, light chain | protein | 214 | 4% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.83 | 0.84 | 105 | empty |
| 2 | 639 | 0.63 | 0.74 | 65 | empty |
| 3 | 94 | 0.48 | 0.81 | 27 | empty |
| 4 | 182 | 0.43 | 0.73 | 22 | empty |
| 5 | 106 | 0.40 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1856 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5I6Z · X-ray structure of the ts2 human serotonin transporter · 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 5I6Z · PDBe 5I6Z · UniProt P31645
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.