MolNFT v1 · #143341 · protein
Anomalous chloride signal reveals the position of sertraline complexed with the serotonin transporter at the central site
6AWQ · Sodium-dependent serotonin transporter: “Anomalous chloride signal reveals the position of sertraline complexed with the serotonin transporter at the…”. X-ray diffraction, 5 ligands (SRE, CLR, NAG), 12 pockets (best druggability…
- PDB
- 6AWQ
- 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 Fab heavy chain; 8B6 antibody Fab…
- UniProt
- P31645, A0A0F7R1P3, A0A0F7R5U8
- Ligands
- SRE, CLR, NAG, NA, CL
- Pockets
- 12 · best druggability 0.84
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 | 69% helix, 1% strand | P31645 |
| B | 8B6 antibody Fab heavy chain | protein | 218 | 4% helix, 52% strand | A0A0F7R1P3 |
| C | 8B6 antibody Fab light chain | protein | 214 | 6% helix, 46% strand | A0A0F7R5U8 |
Ligands and binding sites
- SRE · (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.84 | 0.85 | 118 | SRE |
| 2 | 425 | 0.57 | 0.74 | 44 | empty |
| 3 | 275 | 0.51 | 0.74 | 41 | empty |
| 4 | 118 | 0.44 | 0.76 | 21 | empty |
| 5 | 109 | 0.42 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1812 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6AWQ · Anomalous chloride signal reveals the position of sertraline complexed with the serotonin… · 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 A0A0F7R1P3
- Every structure of UniProt A0A0F7R5U8
- Elsewhere: RCSB PDB 6AWQ · PDBe 6AWQ · UniProt P31645 · UniProt A0A0F7R1P3 · UniProt A0A0F7R5U8
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