MolNFT v1 · #110148 · protein
X-ray structure of drosophila dopamine transporter in complex with reboxetine
4XNX: “X-ray structure of drosophila dopamine transporter in complex with reboxetine”. X-ray diffraction, 6 ligands (CLR, 41X, BGC), 7 pockets (best druggability 0.80). MolNFT v1 #110148 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4XNX
- Type
- protein
- Length
- 966 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter; Antibody fragment light chain; Antibody fragment heavy chain
- UniProt
- A0A0B4KEX2
- Ligands
- CLR, 41X, BGC, GLC, NA, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transporter | protein | 536 | 74% helix, 1% strand | A0A0B4KEX2 |
| L | Antibody fragment light chain | protein | 214 | 7% helix, 53% strand | — |
| H | Antibody fragment heavy chain | protein | 216 | 3% helix, 52% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- 41X · (2R)-2-[(R)-(2-ethoxyphenoxy)(phenyl)methyl]morpholine · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GLC · alpha-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 | 977 | 0.80 | 0.82 | 78 | 41X |
| 2 | 338 | 0.57 | 0.76 | 44 | empty |
| 3 | 88 | 0.41 | 0.78 | 14 | empty |
| 4 | 106 | 0.41 | 0.76 | 22 | empty |
| 5 | 59 | 0.33 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1886 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 563 Ų buried · 19 hydrogen bonds · protein-protein
- A–L · 76 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4XNX · X-ray structure of Drosophila dopamine transporter in complex with reboxetine · 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 4XNX · PDBe 4XNX · UniProt A0A0B4KEX2
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