MolNFT v1 · #110193 · protein
X-ray structure of drosophila dopamine transporter bound to psychostimulant methamphetamine
4XP6: “X-ray structure of drosophila dopamine transporter bound to psychostimulant methamphetamine”. X-ray diffraction, 7 ligands (B40, CLR, Y01), 7 pockets (best druggability 0.76). MolNFT v1 #110193 on GenesisL1: 3D structure, binding…
- PDB
- 4XP6
- Type
- protein
- Length
- 966 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
- B40, CLR, Y01, GLC, NAG, NA, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transporter | protein | 534 | 71% helix, 1% strand | A0A0B4KEX2 |
| L | Antibody fragment heavy chain-protein, 9D5-heavy chain | protein | 213 | 5% helix, 49% strand | — |
| H | Antibody fragment light chain-protein, 9D5-light chain | protein | 219 | 3% helix, 47% strand | — |
Ligands and binding sites
- B40 · (2S)-N-methyl-1-phenylpropan-2-amine · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.76 | 0.78 | 78 | B40 |
| 2 | 347 | 0.58 | 0.76 | 43 | empty |
| 3 | 136 | 0.44 | 0.76 | 19 | empty |
| 4 | 148 | 0.42 | 0.74 | 21 | empty |
| 5 | 119 | 0.42 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1992 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 559 Ų buried · 22 hydrogen bonds · protein-protein
- A–L · 101 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XP6 · X-ray structure of Drosophila dopamine transporter bound to psychostimulant… · 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
- Every structure of UniProt A0A0B4KEX2
- Elsewhere: RCSB PDB 4XP6 · PDBe 4XP6 · UniProt A0A0B4KEX2
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