Research workbench

Human TRPM2 bound to adpr and calcium

Analyse Human TRPM2 bound to adpr and calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PUS
Type: protein
Length: 5,224 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily M member 2
UniProt: O94759
Ligands: APR, CA
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 48% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, B	Transient receptor potential cation channel subfamily M member 2	protein	1306	48% helix, 10% strand	O94759

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 8 copies · chains A, C, D, B
CA · Calcium ion · metal · 4 copies · chains A, C, D, B

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	1077	0.83	0.84	91	empty
2	1059	0.78	0.79	76	empty
3	1058	0.77	0.79	70	empty
4	778	0.77	0.80	61	empty
5	1184	0.76	0.78	93	empty

Interfaces

6 interfaces between chains.

A–D · 1921 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1918 Å² buried · 4 hydrogen bonds · protein-protein
C–B · 1916 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 1912 Å² buried · 4 hydrogen bonds · protein-protein
D–B · 31 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6PUS · Human TRPM2 bound to ADPR and calcium · the same entry in another collection · chain A against A, TM-score 1.00
O94759 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.76

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 O94759
Elsewhere: RCSB PDB 6PUS · PDBe 6PUS · UniProt O94759

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