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Cryo-EM structure of human TRPV6 in nanodiscs

Analyse Cryo-EM structure of human TRPV6 in nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BO8
Type: protein
Length: 2,372 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 6
UniProt: Q9H1D0
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 54% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 6	protein	593	54% helix, 3% strand	Q9H1D0

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	1120	0.85	0.86	74	empty
2	655	0.74	0.80	52	empty
3	82	0.73	0.96	24	empty
4	76	0.72	0.96	23	empty
5	365	0.72	0.83	25	empty

Interfaces

5 interfaces between chains.

B–C · 3374 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 3346 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 3308 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 3306 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 12 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6BO8 · Cryo-EM structure of human TRPV6 in nanodiscs · the same entry in another collection · chain A against A, TM-score 1.00
Q9H1D0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9H1D0
Elsewhere: RCSB PDB 6BO8 · PDBe 6BO8 · UniProt Q9H1D0

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