Research workbench

Cryo-EM structure of TRPV5 (1-660) in nanodisc

Analyse Cryo-EM structure of TRPV5 (1-660) in nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O1N
Type: protein
Length: 2,448 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
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 46% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 5	protein	612	46% helix, 4% strand	Q9XSM3

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	425	0.85	0.92	36	empty
2	256	0.81	0.93	33	empty
3	187	0.80	0.94	29	empty
4	464	0.78	0.85	52	empty
5	369	0.76	0.86	46	empty

Interfaces

6 interfaces between chains.

C–D · 3445 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 3311 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 3295 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 3189 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 35 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6O1N · Cryo-EM structure of TRPV5 (1-660) in nanodisc · 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 0.97

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 Q9XSM3
Elsewhere: RCSB PDB 6O1N · PDBe 6O1N · UniProt Q9XSM3

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