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Cryo-EM structure of full-length TRPV1 at PH6C state

Analyse Cryo-EM structure of full-length TRPV1 at PH6C state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7L2J
Type: protein
Length: 2,116 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: XJ7
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 57% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 1	protein	529	57% helix, 4% strand	O35433

Ligands and binding sites

XJ7 · (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2r,3s,4s,5r, 6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate · ligand · 4 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	274	0.84	0.96	33	empty
2	1035	0.82	0.82	81	XJ7
3	1164	0.81	0.82	101	XJ7
4	1017	0.81	0.82	73	XJ7
5	1011	0.81	0.82	75	XJ7

Interfaces

6 interfaces between chains.

A–D · 2496 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 2468 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 2456 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 2414 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7L2J · Cryo-EM structure of full-length TRPV1 at pH6c 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 7L2J · PDBe 7L2J · UniProt O35433

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