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X-ray structure of drosophila dopamine transporter with net-like mutations (D121G/S426M/F471L) in L-norepinephrine bound form

Analyse X-ray structure of drosophila dopamine transporter with net-like mutations… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M0Z
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 (Fab) 9D5 light chain; Antibody…
UniProt: Q7K4Y6
Ligands: CLR, Y01, LNR, NA, CL
Pockets: 8 · best druggability 0.79

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, 1% strand	Q7K4Y6
L	Antibody fragment (Fab) 9D5 light chain	protein	214	8% helix, 54% strand	—
H	Antibody fragment (Fab) 9D5 heavy chain	protein	219	7% helix, 50% strand	—

Ligands and binding sites

CLR · Cholesterol · ligand · chains A
Y01 · Cholesterol hemisuccinate · ligand · chains A
LNR · L-norepinephrine · 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

8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.79	0.80	92	LNR
2	219	0.50	0.76	36	empty
3	148	0.43	0.75	23	empty
4	167	0.43	0.74	20	empty
5	141	0.43	0.75	22	empty

Interfaces

3 interfaces between chains.

L–H · 1962 Å² buried · 21 hydrogen bonds · protein-protein
A–H · 562 Å² buried · 22 hydrogen bonds · protein-protein
A–L · 78 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6M0Z · X-ray structure of 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 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 6M0Z · PDBe 6M0Z · UniProt Q7K4Y6

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