Research workbench
Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine and 8B6 Fab
Analyse Cryo-EM structure of the wild-type human serotonin transporter complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRH
- Type
- protein
- Length
- 764 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent serotonin transporter; 8B6 antibody, light chain; 8B6 antibody, heavy…
- UniProt
- P31645, A0A0U5BC76
- Ligands
- 8PR, NAG, CL
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 541 | 69% helix, 1% strand | P31645 |
| C | 8B6 antibody, light chain | protein | 106 | 0% helix, 44% strand | A0A0U5BC76 |
| B | 8B6 antibody, heavy chain | protein | 117 | 5% helix, 41% strand | — |
Ligands and binding sites
- 8PR · Paroxetine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- CL · Chloride ion · ion · 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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.84 | 0.87 | 67 | 8PR, LMT |
| 2 | 550 | 0.73 | 0.81 | 58 | empty |
| 3 | 219 | 0.48 | 0.74 | 22 | empty |
| 4 | 124 | 0.40 | 0.75 | 21 | empty |
| 5 | 77 | 0.37 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–B · 839 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 559 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6VRH · Cryo-EM structure of the wild-type human serotonin transporter complexed with paroxetine… · 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
- Every structure of UniProt A0A0U5BC76
- Elsewhere: RCSB PDB 6VRH · PDBe 6VRH · UniProt P31645 · UniProt A0A0U5BC76
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