MolNFT v1 · #187996 · protein

Cryo-EM structure of TRPV5 T709D with PI(4,5)P2 in nanodiscs

7T6Q · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of TRPV5 T709D with PI(4,5)P2 in nanodiscs”. Electron microscopy, 1 ligand (PIO), 20 pockets (best druggability 0.84). MolNFT v1 #187996 on GenesisL1: 3D…

PDB: 7T6Q
Type: protein
Length: 2,424 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: PIO
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 55% 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	606	55% helix, 4% strand	Q9XSM3

Ligands and binding sites

PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 4 copies · chains A, B, C, D

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	984	0.84	0.85	74	empty
2	119	0.78	0.96	26	empty
3	112	0.77	0.97	25	empty
4	112	0.77	0.97	26	empty
5	111	0.76	0.95	25	empty

Interfaces

6 interfaces between chains.

A–B · 3408 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 3400 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 3369 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 3362 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 33 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7T6Q · Cryo-EM structure of TRPV5 T709D with PI(4,5)P2 in nanodiscs · 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 7T6Q · PDBe 7T6Q · UniProt Q9XSM3

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