Research workbench

3.3 ångström structure of mouse TRPM7 with edta

Analyse 3.3 ångström structure of mouse TRPM7 with edta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZX5
Type: protein
Length: 3,256 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily M member 7
EC: 2.7.11.1
UniProt: Q923J1
Ligands: Y01
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 59% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily M member 7 (EC 2.7.11.1)	protein	814	59% helix, 2% strand	Q923J1

Ligands and binding sites

Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, B, D, 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	151	0.80	0.96	17	empty
2	967	0.77	0.79	91	Y01
3	988	0.77	0.79	86	Y01
4	691	0.75	0.81	68	Y01
5	528	0.74	0.82	62	empty

Interfaces

6 interfaces between chains.

C–D · 3064 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 3062 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 3062 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 3055 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 113 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5ZX5 · 3.3 angstrom structure of mouse TRPM7 with EDTA · the same entry in another collection · chain A against A, TM-score 1.00
Q923J1 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q923J1
Elsewhere: RCSB PDB 5ZX5 · PDBe 5ZX5 · UniProt Q923J1

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