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X-ray structure of drosophila dopamine transporter with subsiteb mutations (D121G/S426M) in substrate-free form

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: 6M0F
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, P4G, NA, CL
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sodium-dependent dopamine transporter	protein	534	71% helix, 1% strand	Q7K4Y6
L	Antibody fragment (9D5) light chain	protein	214	5% helix, 49% strand	—
H	Antibody fragment (9D5) heavy chain	protein	219	8% helix, 48% strand	—

Ligands and binding sites

CLR · Cholesterol · ligand · 2 copies · chains A
P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.79	0.81	87	P4G
2	277	0.53	0.75	42	empty
3	156	0.48	0.77	25	empty
4	73	0.44	0.81	21	empty
5	111	0.41	0.76	22	empty

Interfaces

3 interfaces between chains.

L–H · 1945 Å² buried · 21 hydrogen bonds · protein-protein
A–H · 573 Å² buried · 16 hydrogen bonds · protein-protein
A–L · 94 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6M0F · 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 6M0F · PDBe 6M0F · UniProt Q7K4Y6

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