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Human TRPM2 bound to 8-br-cadpr and calcium

Analyse Human TRPM2 bound to 8-br-cadpr and calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PUU
Type: protein
Length: 5,236 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: CV1, CA
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily M member 2	protein	1309	49% helix, 11% strand	O94759

Ligands and binding sites

CV1 · (2R,3R,4S,5R,13R,14S,15R,16R)-24-amino-18-bromo-3,4,14, 15-tetrahydroxy-7,9,11,25,26-pentaoxa-17,19,22-triaza-1-azonia-8,10-diphosphapentacyclo[18.3.1.1^2,5^.1^13, 16^.0^17,21^]hexacosa-1(24),18,20,22-tetraene-8,10-diolate 8,10-dioxide · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1082	0.82	0.83	95	CA
2	1003	0.81	0.82	111	empty
3	1060	0.78	0.80	77	CA
4	1088	0.78	0.80	81	CA
5	1039	0.78	0.80	83	CA

Interfaces

6 interfaces between chains.

C–D · 2360 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 2354 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 2347 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 2342 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 21 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6PUU · Human TRPM2 bound to 8-Br-cADPR 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 0.92

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 6PUU · PDBe 6PUU · UniProt O94759

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