MolNFT v1 · #179397 · protein

Cryo-EM structure of human TRPV6 in the open state

7K4A · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of human TRPV6 in the open state”. Electron microscopy, 3 ligands (PCW, Y01, CA), 20 pockets (best druggability 0.83). MolNFT v1 #179397 on GenesisL1: 3D…

PDB: 7K4A
Type: protein
Length: 2,420 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transient receptor potential cation channel subfamily V member 6
UniProt: Q9H1D0
Ligands: PCW, Y01, CA
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 44% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transient receptor potential cation channel subfamily V member 6	protein	605	44% helix, 3% strand	Q9H1D0

Ligands and binding sites

PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 52 copies · chains A, D, B, C
Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, B, D, C
CA · Calcium ion · metal · 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1093	0.83	0.84	66	empty
2	993	0.79	0.80	68	Y01
3	1059	0.79	0.80	85	Y01
4	1010	0.79	0.80	73	Y01
5	1198	0.77	0.78	75	Y01

Interfaces

6 interfaces between chains.

B–C · 3501 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 3500 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 3494 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 3487 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 32 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7K4A · Cryo-EM structure of human TRPV6 in the open state · the same entry in another collection · chain A against A, TM-score 1.00
Q9H1D0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9H1D0
Elsewhere: RCSB PDB 7K4A · PDBe 7K4A · UniProt Q9H1D0

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