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Cryo-EM structure of human TRPV6-Y467A in amphipols

Analyse Cryo-EM structure of human TRPV6-Y467A in amphipols in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6D7S
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 · 55% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 6	protein	593	55% helix, 2% 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	1164	0.85	0.86	81	empty
2	686	0.76	0.81	44	empty
3	677	0.76	0.81	48	empty
4	685	0.76	0.81	44	empty
5	695	0.76	0.81	47	empty

Interfaces

6 interfaces between chains.

C–D · 3426 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 3413 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 3383 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 3348 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 27 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6D7S · Cryo-EM structure of human TRPV6-Y467A in amphipols · 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 6D7S · PDBe 6D7S · UniProt Q9H1D0

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