Research workbench
X-ray structure of drosophila dopamine transporter bound to neurotransmitter dopamine
Analyse X-ray structure of drosophila dopamine transporter bound to neurotransmitter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XP1
- Type
- protein
- Length
- 968 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dopamine transporter, isoform B; Antibody fragment light chain; Antibody fragment heavy…
- UniProt
- A0A0B4KEX2
- Ligands
- P4G, LDP, Y01, CLR, GLC, NAG, NA, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dopamine transporter, isoform B | protein | 535 | 73% helix, 1% strand | A0A0B4KEX2 |
| L | Antibody fragment light chain | protein | 214 | 7% helix, 53% strand | — |
| H | Antibody fragment heavy chain | protein | 219 | 7% helix, 49% strand | — |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains A
- LDP · L-dopamine · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · 3 copies · chains A, L
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.78 | 0.80 | 80 | LDP, EDO |
| 2 | 229 | 0.50 | 0.75 | 39 | empty |
| 3 | 158 | 0.45 | 0.75 | 23 | empty |
| 4 | 159 | 0.43 | 0.75 | 23 | empty |
| 5 | 52 | 0.40 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1945 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 562 Ų buried · 22 hydrogen bonds · protein-protein
- A–L · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XP1 · X-ray structure of Drosophila dopamine transporter bound to neurotransmitter dopamine · 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 4XP1 · PDBe 4XP1 · UniProt A0A0B4KEX2
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