Research workbench
Anomalous chloride signal reveals the position of sertraline complexed with the serotonin transporter at the central site
Analyse Anomalous chloride signal reveals the position of sertraline complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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