Research workbench

PI3P and calcium bound full-length TRPY1 in detergent

Analyse PI3P and calcium bound full-length TRPY1 in detergent in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WHG
Type: protein
Length: 2,092 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calcium channel YVC1
UniProt: Q12324
Ligands: PWE, CA
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Calcium channel YVC1	protein	523	68% helix, 1% strand	Q12324

Ligands and binding sites

PWE · (2R)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1s,2s,3s,4s,5s, 6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl hexadecanoate · ligand · 4 copies · chains A, D, B, C
CA · Calcium ion · metal · 8 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	687	0.84	0.88	53	empty
2	876	0.75	0.78	71	PWE
3	928	0.75	0.78	76	PWE
4	969	0.75	0.77	79	PWE
5	859	0.75	0.78	73	PWE

Interfaces

6 interfaces between chains.

C–D · 3001 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 2998 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2997 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 2994 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 53 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6WHG · PI3P and calcium bound full-length TRPY1 in detergent · the same entry in another collection · chain A against A, TM-score 1.00
Q12324 · AlphaFold monomer V2.0 prediction for calcium channel YVC1 (Q12324) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q12324
Elsewhere: RCSB PDB 6WHG · PDBe 6WHG · UniProt Q12324

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.