MolNFT v1 · #147020 · protein
Cryo-EM structure of the TS2-active human serotonin transporter in complex with 15B8 Fab and 8B6 scfv bound to ibogaine
6DZY · Sodium-dependent serotonin transporter: “Cryo-EM structure of the TS2-active human serotonin transporter in complex with 15B8 Fab and 8B6 scfv bound…”. Electron microscopy, 2 ligands (HJM, NAG), 15 pockets (best druggability 0.81).…
- PDB
- 6DZY
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent serotonin transporter; 15B8 antibody heavy chain; 15B8 antibody light…
- UniProt
- P31645
- Ligands
- HJM, NAG
- Pockets
- 15 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 537 | 72% helix, 1% strand | P31645 |
| H | 15B8 antibody heavy chain | protein | 118 | 10% helix, 42% strand | — |
| L | 15B8 antibody light chain | protein | 110 | 3% helix, 46% strand | — |
| V | 8B6 antibody single chain | protein | 223 | 7% helix, 46% strand | — |
Ligands and binding sites
- HJM · (5beta)-12-methoxyibogamine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.81 | 0.83 | 87 | HJM, LMT |
| 2 | 603 | 0.77 | 0.83 | 52 | empty |
| 3 | 62 | 0.66 | 0.94 | 17 | empty |
| 4 | 418 | 0.64 | 0.78 | 34 | empty |
| 5 | 124 | 0.63 | 0.87 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–V · 1181 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 929 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 582 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 269 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6DZY · Cryo-EM structure of the ts2-active human serotonin transporter in complex with 15B8 Fab… · 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 0.98
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 6DZY · PDBe 6DZY · UniProt P31645
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