Research workbench
X-ray structure of drosophila dopamine transporter with subsiteb mutations (D121G/S426M) bound to rti-55
Analyse X-ray structure of drosophila dopamine transporter with subsiteb mutations… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XPF
- Type
- protein
- Length
- 961 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dopamine transporter-protein; Antibody fragment heavy chain-protein, 9D5-heavy chain…
- Ligands
- CLR, P4G, 42F, NA, CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dopamine transporter-protein | protein | 532 | 70% helix, 2% strand | — |
| L | Antibody fragment heavy chain-protein, 9D5-heavy chain | protein | 214 | 4% helix, 51% strand | — |
| H | Antibody fragment light chain-protein, 9D5-light chain | protein | 215 | 6% helix, 48% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains A
- 42F · methyl (1R,2S,3S,5S)-3-(4-iodophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- DMU · Decyl-beta-D-maltopyranoside · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.78 | 0.79 | 88 | P4G, 42F |
| 2 | 313 | 0.56 | 0.76 | 38 | empty |
| 3 | 118 | 0.43 | 0.77 | 21 | empty |
| 4 | 73 | 0.43 | 0.81 | 13 | empty |
| 5 | 98 | 0.40 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1907 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 648 Ų buried · 20 hydrogen bonds · protein-protein
- A–L · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4XPF · 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
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4XPF · PDBe 4XPF
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