Research workbench
Cryo-EM structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation
Analyse Cryo-EM structure of the wild-type human serotonin transporter in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DZZ
- Type
- protein
- Length
- 768 residues
- Chains
- 3
- 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
- 12 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 540 | 59% helix, 1% strand | P31645 |
| B | 15B8 antibody heavy chain | protein | 118 | 3% helix, 42% strand | — |
| C | 15B8 antibody light chain | protein | 110 | 3% helix, 30% 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.84 | 0.88 | 77 | HJM |
| 2 | 292 | 0.65 | 0.81 | 50 | empty |
| 3 | 378 | 0.59 | 0.76 | 39 | empty |
| 4 | 193 | 0.57 | 0.80 | 30 | empty |
| 5 | 131 | 0.51 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 967 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6DZZ · Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine… · 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 0.90
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 6DZZ · PDBe 6DZZ · UniProt P31645
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