MolNFT v1 · #156435 · protein
X-ray structure of a drosophila dopamine transporter with net-like mutations (D121G/S426M/F471L) in tramadol bound form
6M47 · Sodium-dependent dopamine transporter: “X-ray structure of a drosophila dopamine transporter with net-like mutations (D121G/S426M/F471L) in tramadol…”. X-ray diffraction, 7 ligands (CLR, Y01, F1U), 7 pockets (best druggability…
- PDB
- 6M47
- Type
- protein
- Length
- 967 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent dopamine transporter; Antibody fragment 9D5 light chain; Antibody…
- UniProt
- Q7K4Y6
- Ligands
- CLR, Y01, F1U, D10, GLC, NA, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent dopamine transporter | protein | 534 | 72% helix, 2% strand | Q7K4Y6 |
| L | Antibody fragment 9D5 light chain | protein | 214 | 7% helix, 53% strand | — |
| H | Antibody fragment heavy chain | protein | 219 | 4% helix, 47% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- F1U · (1S,2S)-2-[(dimethylamino)methyl]-1-(3-methoxyphenyl) cyclohexan-1-ol · ligand · chains A
- D10 · Decane · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · 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 | 968 | 0.80 | 0.81 | 87 | F1U |
| 2 | 418 | 0.59 | 0.76 | 56 | empty |
| 3 | 152 | 0.44 | 0.75 | 23 | empty |
| 4 | 110 | 0.39 | 0.75 | 24 | empty |
| 5 | 56 | 0.36 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1996 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 599 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6M47 · X-ray structure of a Drosophila dopamine transporter with NET-like mutations… · 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 6M47 · PDBe 6M47 · UniProt Q7K4Y6
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