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Structure of TRPV5 in complex with econazole

Analyse Structure of TRPV5 in complex with econazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B5V
Type: protein
Length: 2,356 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 5
UniProt: Q9XSM3
Ligands: ECL, CA
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 47% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, C	Transient receptor potential cation channel subfamily V member 5	protein	589	47% helix, 1% strand	Q9XSM3

Ligands and binding sites

ECL · 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl) ethyl]-1H-imidazole · ligand · 4 copies · chains A, C, B, D
CA · Calcium ion · metal · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	733	0.86	0.90	60	CA
2	1061	0.86	0.87	113	empty
3	1132	0.86	0.87	120	empty
4	939	0.82	0.83	81	empty
5	996	0.81	0.82	85	empty

Interfaces

6 interfaces between chains.

A–B · 2681 Å² buried · 9 hydrogen bonds · protein-protein
D–C · 2652 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 2645 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 2599 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 39 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6B5V · Structure of TRPV5 in complex with econazole · the same entry in another collection · chain A against A, TM-score 1.00
Q9XSM3 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q9XSM3
Elsewhere: RCSB PDB 6B5V · PDBe 6B5V · UniProt Q9XSM3

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