Research workbench
X-ray structure of thermostabilized drosophila dopamine transporter with GABA TRANSPORTER1-like substitutions in the binding site, in complex with SKF89976A
Analyse X-ray structure of thermostabilized drosophila dopamine transporter with GABA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WLW
- Type
- protein
- Length
- 969 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent dopamine transporter; Antibody fragment light chain; Antibody fragment…
- UniProt
- Q7K4Y6
- Ligands
- 1WR, Y01, CLR, NA, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent dopamine transporter | protein | 536 | 72% helix, 1% strand | Q7K4Y6 |
| L | Antibody fragment light chain | protein | 214 | 7% helix, 51% strand | — |
| H | Antibody fragment heavy chain | protein | 219 | 8% helix, 50% strand | — |
Ligands and binding sites
- 1WR · (3S)-1-(4,4-diphenylbut-3-enyl)piperidine-3-carboxylic acid · ligand · 2 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- DMU · Decyl-beta-D-maltopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.80 | 0.81 | 85 | 1WR |
| 2 | 448 | 0.61 | 0.76 | 44 | empty |
| 3 | 123 | 0.46 | 0.78 | 23 | empty |
| 4 | 78 | 0.31 | 0.74 | 17 | empty |
| 5 | 57 | 0.30 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2104 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 590 Ų buried · 23 hydrogen bonds · protein-protein
- A–L · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7WLW · X-ray structure of thermostabilized Drosophila dopamine transporter with GABA… · 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 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 Q7K4Y6
- Elsewhere: RCSB PDB 7WLW · PDBe 7WLW · UniProt Q7K4Y6
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