Research workbench

Cryo-EM structure of full-length TRPV1 at PH6A state

Analyse Cryo-EM structure of full-length TRPV1 at PH6A state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7L2I
Type: protein
Length: 2,124 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 1
UniProt: O35433
Ligands: XJA
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 58% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, B	Transient receptor potential cation channel subfamily V member 1	protein	531	58% helix, 4% strand	O35433

Ligands and binding sites

XJA · (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1s,2r,3r,4r,5r, 6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate · ligand · 4 copies · chains A, D, C, 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	273	0.84	0.96	31	empty
2	1013	0.82	0.83	87	XJA
3	1028	0.80	0.81	76	XJA
4	1194	0.80	0.81	96	XJA
5	1146	0.79	0.81	88	XJA

Interfaces

6 interfaces between chains.

A–B · 2638 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 2601 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 2586 Å² buried · 10 hydrogen bonds · protein-protein
C–B · 2566 Å² buried · 8 hydrogen bonds · protein-protein
D–B · 32 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7L2I · Cryo-EM structure of full-length TRPV1 at pH6a state · the same entry in another collection · chain A against A, TM-score 1.00
O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O35433
Elsewhere: RCSB PDB 7L2I · PDBe 7L2I · UniProt O35433

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