MolNFT v1 · #124066 · protein

Cryoem structure of the human polycystin-2/PKD2 TRP channel

5K47: “Cryoem structure of the human polycystin-2/PKD2 TRP channel”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #124066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K47
Type: protein
Length: 1,936 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polycystin-2
UniProt: Q13563
Ligands: NAG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 1 distinct chain · 56% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Polycystin-2	protein	484	56% helix, 10% strand	Q13563

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	271	0.86	0.97	28	empty
2	1116	0.85	0.85	125	empty
3	1109	0.85	0.85	122	empty
4	482	0.79	0.86	59	empty
5	916	0.79	0.81	75	empty

Interfaces

6 interfaces between chains.

A–B · 3616 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 3604 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 3604 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 3596 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 70 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan (N-glycosylation).

Compared structures

5K47 · CryoEM structure of the human Polycystin-2/PKD2 TRP channel · the same entry in another collection · chain A against A, TM-score 1.00
Q13563 · AlphaFold monomer V2.0 prediction for polycystin-2 (Q13563) · 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 Q13563
Elsewhere: RCSB PDB 5K47 · PDBe 5K47 · UniProt Q13563

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