Research workbench
Anomalous bromine signal reveals the position of br-paroxetine complexed with the serotonin transporter at the central site
Analyse Anomalous bromine signal reveals the position of br-paroxetine complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W2B
- 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 heavy chain antibody fragment; 8B6 light…
- UniProt
- P31645
- Ligands
- RFS, NAG
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 544 | 69% helix, 1% strand | P31645 |
| B | 8B6 heavy chain antibody fragment | protein | 218 | 3% helix, 50% strand | — |
| C | 8B6 light chain antibody fragment | protein | 214 | 6% helix, 47% strand | — |
Ligands and binding sites
- RFS · Br-paroxetine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.85 | 0.86 | 84 | RFS |
| 2 | 332 | 0.62 | 0.78 | 46 | empty |
| 3 | 387 | 0.55 | 0.74 | 47 | empty |
| 4 | 76 | 0.45 | 0.82 | 25 | empty |
| 5 | 168 | 0.42 | 0.73 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1804 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6W2B · Anomalous bromine signal reveals the position of Br-paroxetine complexed with the… · 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 6W2B · PDBe 6W2B · UniProt P31645
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