MolNFT v1 · #160128 · protein

ZINC9155420-bound TRPV5 in nanodiscs

6PBF · Transient receptor potential cation channel subfamily V…: “ZINC9155420-bound TRPV5 in nanodiscs”. Electron microscopy, 1 ligand (O6V), 20 pockets (best druggability 0.84). MolNFT v1 #160128 on GenesisL1: 3D structure, binding sites…

PDB: 6PBF
Type: protein
Length: 2,392 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: O6V
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 57% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 5	protein	598	57% helix, 3% strand	Q9XSM3

Ligands and binding sites

O6V · (1S)-1-(4-oxo-5-phenyl-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)ethyl [(2S)-3-oxo-3,4-dihydro-2H-1,4-benzothiazin-2-yl]acetate · ligand · 4 copies · chains A, C, B, 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	303	0.84	0.94	36	empty
2	338	0.82	0.92	51	empty
3	263	0.81	0.93	23	empty
4	332	0.80	0.90	58	empty
5	348	0.80	0.89	59	empty

Interfaces

6 interfaces between chains.

A–B · 3381 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 3361 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 3344 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 3324 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 35 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6PBF · ZINC9155420-bound TRPV5 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 0.97

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 6PBF · PDBe 6PBF · UniProt Q9XSM3

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