MolNFT v1 · #156395 · protein
X-ray structure of a functional drosophila dopamine transporter in L- norepinephrine bound form
6M2R · Sodium-dependent dopamine transporter: “X-ray structure of a functional drosophila dopamine transporter in L- norepinephrine bound form”. X-ray diffraction, 6 ligands (D10, Y01, CLR), 6 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6M2R
- Type
- protein
- Length
- 969 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
- D10, Y01, CLR, LNR, NA, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent dopamine transporter | protein | 536 | 74% helix, 2% strand | Q7K4Y6 |
| L | Antibody fragment 9D5 light chain | protein | 214 | 7% helix, 54% strand | — |
| H | Antibody fragment 9D5 heavy chain | protein | 219 | 5% helix, 51% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · 3 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- LNR · L-norepinephrine · ligand · chains A
- NA · Sodium ion · metal · 4 copies · chains A, L
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.80 | 0.82 | 76 | LNR, D10 |
| 2 | 539 | 0.64 | 0.76 | 55 | empty |
| 3 | 182 | 0.50 | 0.77 | 27 | empty |
| 4 | 53 | 0.35 | 0.79 | 13 | empty |
| 5 | 55 | 0.29 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2005 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 601 Ų buried · 23 hydrogen bonds · protein-protein
- A–L · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6M2R · X-ray structure of a functional Drosophila dopamine transporter in L-norepinephrine bound… · 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 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 Q7K4Y6
- Elsewhere: RCSB PDB 6M2R · PDBe 6M2R · UniProt Q7K4Y6
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