MolNFT v1 · #167999 · protein
Anomalous iodine signal reveals the position of I-paroxetine complexed with the serotonin transporter at the central site
6W2C · Sodium-dependent serotonin transporter: “Anomalous iodine signal reveals the position of I-paroxetine complexed with the serotonin transporter at the…”. X-ray diffraction, 1 ligand (RFY), 11 pockets (best druggability 0.83). MolNFT…
- PDB
- 6W2C
- 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
- RFY
- Pockets
- 11 · best druggability 0.83
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
- RFY · I-paroxetine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.83 | 0.84 | 90 | RFY |
| 2 | 473 | 0.63 | 0.76 | 52 | empty |
| 3 | 394 | 0.55 | 0.74 | 42 | empty |
| 4 | 287 | 0.50 | 0.74 | 35 | empty |
| 5 | 79 | 0.45 | 0.82 | 25 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1805 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6W2C · Anomalous iodine signal reveals the position of I-paroxetine 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 0.98
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 6W2C · PDBe 6W2C · UniProt P31645
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