MolNFT v1 · #110216 · protein
X-ray structure of drosophila dopamine transporter with subsiteb mutations D121G/S426M and EL2 deletion of 162-201 in complex with substrate analogue 3,4 dichlorophen ethylamine
4XPT: “X-ray structure of drosophila dopamine transporter with subsiteb mutations D121G/S426M and EL2 deletion of…”. X-ray diffraction, 8 ligands (Y01, 42J, CLR), 9 pockets (best druggability 0.83). MolNFT v1 #110216 on GenesisL1: 3D…
- PDB
- 4XPT
- Type
- protein
- Length
- 968 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dopamine transporter; Antibody fragment light chain; Antibody fragment heavy chain
- UniProt
- Q7K4Y6
- Ligands
- Y01, 42J, CLR, BGC, GLC, NAG, NA, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dopamine transporter | protein | 535 | 72% helix, 2% strand | Q7K4Y6 |
| L | Antibody fragment light chain | protein | 214 | 6% helix, 49% strand | — |
| H | Antibody fragment heavy chain | protein | 219 | 4% helix, 48% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- 42J · 2-(3,4-dichlorophenyl)ethanamine · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · 5 copies · chains A, L
- GLC · alpha-D-glucopyranose · sugar · 5 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.83 | 0.84 | 113 | empty |
| 2 | 82 | 0.75 | 0.97 | 19 | 42J |
| 3 | 333 | 0.74 | 0.85 | 43 | BGC, GLC |
| 4 | 97 | 0.52 | 0.83 | 21 | empty |
| 5 | 124 | 0.44 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1987 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 728 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 240 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4XPT · X-ray structure of Drosophila dopamine transporter with subsiteB mutations D121G/S426M… · 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 4XPT · PDBe 4XPT · UniProt Q7K4Y6
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