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Cryo-electron microscopy structure of a TRPML3 ion channel

Analyse Cryo-electron microscopy structure of a TRPML3 ion channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W3S
Type: protein
Length: 1,940 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucolipin-3 isoform 1
UniProt: F6RG56
Ligands: Y01, 3PE, NA
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 57% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mucolipin-3 isoform 1	protein	485	57% helix, 15% strand	F6RG56

Ligands and binding sites

Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, B, C, D
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains A, B, D, C
NA · Sodium ion · metal · 6 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	534	0.84	0.90	57	NA
2	709	0.74	0.80	73	empty
3	694	0.74	0.80	80	empty
4	752	0.73	0.79	84	empty
5	719	0.72	0.78	57	empty

Interfaces

6 interfaces between chains.

A–C · 3576 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 3575 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 3567 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 3553 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 14 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5W3S · Cryo-electron microscopy structure of a TRPML3 ion channel · the same entry in another collection · chain A against A, TM-score 1.00
F6RG56 · AlphaFold monomer V2.0 prediction for mucolipin-3 (F6RG56) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 F6RG56
Elsewhere: RCSB PDB 5W3S · PDBe 5W3S · UniProt F6RG56

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