MolNFT v1 · #182638 · protein

Cryo-EM structure of minimal TRPV1 with rtx bound in C2 state

7MZD · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of minimal TRPV1 with rtx bound in C2 state”. Electron microscopy, 2 ligands (6EU, NA), 20 pockets (best druggability 0.88). MolNFT v1 #182638 on…

PDB: 7MZD
Type: protein
Length: 2,128 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: 6EU, NA
Pockets: 20 · best druggability 0.88

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B, C	Transient receptor potential cation channel subfamily V member 1	protein	532	58% helix, 4% strand	O35433

Ligands and binding sites

6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
NA · Sodium ion · metal · 2 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.88	0.88	83	NA
2	154	0.74	0.91	20	empty
3	336	0.70	0.83	35	empty
4	339	0.70	0.82	35	empty
5	327	0.69	0.83	30	empty

Interfaces

6 interfaces between chains.

A–B · 2714 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 2695 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 2688 Å² buried · 10 hydrogen bonds · protein-protein
D–C · 2682 Å² buried · 13 hydrogen bonds · protein-protein
D–B · 29 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7MZD · Cryo-EM structure of minimal TRPV1 with RTX bound in C2 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 7MZD · PDBe 7MZD · UniProt O35433

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