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Cryo-EM structure of TRPV5 W583A in nanodisc

Analyse Cryo-EM structure of TRPV5 W583A in nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O1U
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 5
UniProt: Q9XSM3
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 55% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 5	protein	614	55% helix, 5% strand	Q9XSM3

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	833	0.85	0.87	63	empty
2	111	0.78	0.97	27	empty
3	104	0.77	0.97	27	empty
4	97	0.77	0.97	27	empty
5	377	0.74	0.85	40	empty

Interfaces

6 interfaces between chains.

C–D · 3384 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 3367 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 3358 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 3342 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 31 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6O1U · Cryo-EM structure of TRPV5 W583A 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 0.99

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 6O1U · PDBe 6O1U · UniProt Q9XSM3

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