MolNFT v1 · #110196 · protein
X-ray structure of drosophila dopamine transporter bound to psychostimulant D-amphetamine
4XP9: “X-ray structure of drosophila dopamine transporter bound to psychostimulant D-amphetamine”. X-ray diffraction, 8 ligands (P4G, Y01, CLR), 9 pockets (best druggability 0.76). MolNFT v1 #110196 on GenesisL1: 3D structure, binding…
- PDB
- 4XP9
- Type
- protein
- Length
- 969 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
- A0A0B4KEX2
- Ligands
- P4G, Y01, CLR, 1WE, GLC, NAG, NA, CL
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Transporter | protein | 537 | 75% helix, 1% strand | A0A0B4KEX2 |
| L | Antibody fragment heavy chain-protein, 9D5-heavy chain | protein | 213 | 7% helix, 54% strand | — |
| H | Antibody fragment light chain-protein, 9D5-light chain | protein | 219 | 5% helix, 47% strand | — |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains C
- Y01 · Cholesterol hemisuccinate · ligand · chains C
- CLR · Cholesterol · ligand · chains C
- 1WE · (2S)-1-phenylpropan-2-amine · ligand · chains C
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- NA · Sodium ion · metal · 2 copies · chains C
- CL · Chloride ion · ion · chains C
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.76 | 0.79 | 82 | 1WE |
| 2 | 213 | 0.51 | 0.77 | 38 | empty |
| 3 | 160 | 0.49 | 0.77 | 22 | empty |
| 4 | 158 | 0.46 | 0.76 | 22 | empty |
| 5 | 92 | 0.45 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1946 Ų buried · 21 hydrogen bonds · protein-protein
- C–H · 594 Ų buried · 19 hydrogen bonds · protein-protein
- C–L · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XP9 · X-ray structure of Drosophila dopamine transporter bound to psychostimulant D-amphetamine · the same entry in another collection · chain C against C, 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 A0A0B4KEX2
- Elsewhere: RCSB PDB 4XP9 · PDBe 4XP9 · UniProt A0A0B4KEX2
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