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Structure of human TRPML1 with ml-SI3

Analyse Structure of human TRPML1 with ml-SI3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MGL
Type: protein
Length: 1,888 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucolipin-1
UniProt: Q9GZU1
Ligands: ZB4, 3PE
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 58% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Mucolipin-1	protein	472	58% helix, 12% strand	Q9GZU1

Ligands and binding sites

ZB4 · N-{(1S,2S)-2-[4-(2-methoxyphenyl)piperazin-1-yl]cyclohexyl}benzenesulfonamide · ligand · 4 copies · chains A, D, B, C
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	475	0.87	0.94	36	empty
2	938	0.75	0.78	97	empty
3	888	0.75	0.78	84	empty
4	843	0.74	0.78	78	empty
5	789	0.74	0.79	76	empty

Interfaces

6 interfaces between chains.

A–D · 3672 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 3625 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 3607 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 3571 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7MGL · Structure of human TRPML1 with ML-SI3 · 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 0.97

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 Q9GZU1
Elsewhere: RCSB PDB 7MGL · PDBe 7MGL · UniProt Q9GZU1

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