MolNFT v1 · #147018 · protein
Cryo-EM structure of the TS2-inactive human serotonin transporter in complex with paroxetine and 15B8 Fab and 8B6 scfv
6DZW · Sodium-dependent serotonin transporter: “Cryo-EM structure of the TS2-inactive human serotonin transporter in complex with paroxetine and 15B8 Fab and…”. Electron microscopy, 2 ligands (8PR, NAG), 17 pockets (best druggability…
- PDB
- 6DZW
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent serotonin transporter; 8B6 antibody single chain; 15B8 antibody heavy…
- UniProt
- P31645
- Ligands
- 8PR, NAG
- Pockets
- 17 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 537 | 68% helix, 1% strand | P31645 |
| V | 8B6 antibody single chain | protein | 223 | 3% helix, 39% strand | — |
| H | 15B8 antibody heavy chain | protein | 118 | 3% helix, 47% strand | — |
| L | 15B8 antibody light chain | protein | 110 | 3% helix, 46% strand | — |
Ligands and binding sites
- 8PR · Paroxetine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.87 | 0.89 | 93 | 8PR |
| 2 | 297 | 0.58 | 0.77 | 27 | empty |
| 3 | 119 | 0.56 | 0.84 | 26 | empty |
| 4 | 75 | 0.54 | 0.86 | 17 | empty |
| 5 | 234 | 0.54 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–V · 1131 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 885 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 544 Ų buried · 3 hydrogen bonds · protein-protein
- A–L · 229 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6DZW · Cryo-EM structure of the ts2-inactive human serotonin transporter in complex with… · 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 0.97
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 6DZW · PDBe 6DZW · UniProt P31645
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