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Cryo-EM structure of human TRPML1 with PI45P2

Analyse Cryo-EM structure of human TRPML1 with PI45P2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E7Y
Type: protein
Length: 1,900 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucolipin-1
UniProt: Q9GZU1
Ligands: PIO
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 46% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mucolipin-1	protein	475	46% helix, 12% strand	Q9GZU1

Ligands and binding sites

PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 4 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	369	0.86	0.95	35	empty
2	1065	0.77	0.79	90	empty
3	1107	0.77	0.79	95	empty
4	1118	0.77	0.79	97	empty
5	1101	0.77	0.79	92	empty

Interfaces

6 interfaces between chains.

A–B · 3699 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 3693 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 3686 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 3685 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 36 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6E7Y · cryo-EM structure of human TRPML1 with PI45P2 · 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 0.96

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 6E7Y · PDBe 6E7Y · UniProt Q9GZU1

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