Research workbench
X-ray structure of drosophila dopamine transporter bound to 3, 4DICHLOROPHENETHYLAMINE
Analyse X-ray structure of drosophila dopamine transporter bound to 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XPA
- Type
- protein
- Length
- 967 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…
- Ligands
- CLR, 42J, BGC, GLC, NA, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transporter | protein | 534 | 74% helix, 1% strand | — |
| L | Antibody fragment heavy chain-protein, 9D5-heavy chain | protein | 214 | 7% helix, 52% strand | — |
| H | Antibody fragment light chain-protein, 9D5-light chain | protein | 219 | 5% helix, 50% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- 42J · 2-(3,4-dichlorophenyl)ethanamine · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.74 | 0.78 | 71 | empty |
| 2 | 64 | 0.73 | 0.98 | 16 | 42J |
| 3 | 463 | 0.62 | 0.76 | 42 | empty |
| 4 | 156 | 0.49 | 0.77 | 19 | empty |
| 5 | 87 | 0.45 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2004 Ų buried · 23 hydrogen bonds · protein-protein
- A–H · 582 Ų buried · 24 hydrogen bonds · protein-protein
- A–L · 108 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4XPA · X-ray structure of Drosophila dopamine transporter bound to 3,4dichlorophenethylamine · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4XPA · PDBe 4XPA
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