Research workbench

2-apb bound state of MTRPV2

Analyse 2-apb bound state of MTRPV2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7YEP
Type: protein
Length: 2,456 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 2
UniProt: Q9WTR1
Ligands: FZ4
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 56% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 2	protein	614	56% helix, 5% strand	Q9WTR1

Ligands and binding sites

FZ4 · 2-aminoethyl diphenylborinate · 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.83	0.98	20	empty
2	365	0.83	0.91	42	empty
3	366	0.82	0.91	40	empty
4	355	0.81	0.91	42	empty
5	368	0.81	0.90	41	empty

Interfaces

6 interfaces between chains.

A–D · 2731 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 2725 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 2718 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 2710 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 68 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7YEP · 2-APB bound state of mTRPV2 · the same entry in another collection · chain A against A, TM-score 1.00
Q9WTR1 · 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 Q9WTR1
Elsewhere: RCSB PDB 7YEP · PDBe 7YEP · UniProt Q9WTR1

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