MolNFT v1 · #155731 · protein

Cryo-EM structure of TRPV3 in lipid nanodisc

6LGP · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of TRPV3 in lipid nanodisc”. Electron microscopy, 2 ligands (POV, PLC), 20 pockets (best druggability 0.85). MolNFT v1 #155731 on GenesisL1: 3D structure…

PDB: 6LGP
Type: protein
Length: 2,488 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 3
UniProt: Q8K424
Ligands: POV, PLC
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 55% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 3	protein	622	55% helix, 4% strand	Q8K424

Ligands and binding sites

POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 16 copies · chains A, D, B, C
PLC · Diundecyl phosphatidyl choline · ligand · 12 copies · chains A, B, D, 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	425	0.85	0.93	32	empty
2	225	0.80	0.94	22	empty
3	1023	0.79	0.80	85	POV
4	1021	0.79	0.80	81	POV
5	1026	0.79	0.80	83	POV

Interfaces

6 interfaces between chains.

A–D · 2966 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 2959 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2956 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 2955 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 26 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6LGP · cryo-EM structure of TRPV3 in lipid nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
Q8K424 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q8K424
Elsewhere: RCSB PDB 6LGP · PDBe 6LGP · UniProt Q8K424

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