Research workbench
X-ray structure of drosophila dopamine transporter with subsiteb mutations (D121G/S426M) bound to cocaine
Analyse X-ray structure of drosophila dopamine transporter with subsiteb mutations… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XPB
- Type
- protein
- Length
- 961 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter; Antibody fragment heavy chain-protein, 9D5-heavy chain; Antibody fragment…
- UniProt
- Q7K4Y6
- Ligands
- CLR, COC, BGC, GLC, NA, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transporter | protein | 532 | 72% helix, 2% strand | Q7K4Y6 |
| L | Antibody fragment heavy chain-protein, 9D5-heavy chain | protein | 214 | 6% helix, 53% strand | — |
| H | Antibody fragment light chain-protein, 9D5-light chain | protein | 215 | 4% helix, 51% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- COC · Cocaine · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A, L
- 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.79 | 0.85 | 52 | COC |
| 2 | 705 | 0.74 | 0.80 | 65 | empty |
| 3 | 200 | 0.57 | 0.80 | 40 | empty |
| 4 | 133 | 0.50 | 0.80 | 23 | empty |
| 5 | 100 | 0.45 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1929 Ų buried · 21 hydrogen bonds · protein-protein
- A–L · 631 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 182 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4XPB · X-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7K4Y6 · AlphaFold monomer V2.0 prediction for sodium-dependent dopamine transporter (Q7K4Y6) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q7K4Y6
- Elsewhere: RCSB PDB 4XPB · PDBe 4XPB · UniProt Q7K4Y6
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