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Human TRPML1 channel structure in agonist-bound open conformation

Analyse Human TRPML1 channel structure in agonist-bound open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WJ9
Type: protein
Length: 1,916 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucolipin-1
UniProt: Q9GZU1
Ligands: AQV
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mucolipin-1	protein	479	57% helix, 13% strand	Q9GZU1

Ligands and binding sites

AQV · 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione · ligand · 4 copies · chains A, D, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	664	0.82	0.86	56	empty
2	976	0.78	0.79	77	empty
3	854	0.77	0.80	71	empty
4	804	0.76	0.80	76	empty
5	561	0.73	0.81	54	empty

Interfaces

6 interfaces between chains.

B–C · 3615 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 3607 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 3586 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 3563 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 26 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5WJ9 · Human TRPML1 channel structure in agonist-bound open conformation · the same entry in another collection · chain A against A, TM-score 1.00
Q9GZU1 · AlphaFold monomer V2.0 prediction for mucolipin-1 (Q9GZU1) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q9GZU1
Elsewhere: RCSB PDB 5WJ9 · PDBe 5WJ9 · UniProt Q9GZU1

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