MolNFT v1 · #146615 · protein

PI(4,5)P2 bound full-length RBTRPV5

6DMU · Transient receptor potential cation channel subfamily V…: “PI(4,5)P2 bound full-length RBTRPV5”. Electron microscopy, 1 ligand (PIO), 20 pockets (best druggability 0.83). MolNFT v1 #146615 on GenesisL1: 3D structure, binding sites…

PDB: 6DMU
Type: protein
Length: 2,428 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 0.83

Structure

electron microscopy · 1 distinct chain · 57% 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	607	57% helix, 5% 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	968	0.83	0.84	94	empty
2	935	0.83	0.85	89	empty
3	959	0.83	0.84	88	empty
4	900	0.83	0.84	63	empty
5	457	0.82	0.89	45	empty

Interfaces

4 interfaces between chains.

A–B · 2898 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 2893 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 2892 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 2891 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6DMU · PI(4,5)P2 bound full-length rbTRPV5 · 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 0.94

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 6DMU · PDBe 6DMU · UniProt Q9XSM3

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