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Cryo-EM structure of polycystic kidney disease protein 2 (PKD2), residues 198-703

Analyse Cryo-EM structure of polycystic kidney disease protein 2 (PKD2), residues… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T4D
Type: protein
Length: 1,852 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HPKD:198-703, polycystin-2
UniProt: Q13563
Ligands: NAG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 55% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	HPKD:198-703, polycystin-2	protein	463	55% helix, 13% strand	Q13563

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	331	0.87	0.97	34	empty
2	1041	0.87	0.88	139	empty
3	1053	0.86	0.87	136	empty
4	1050	0.86	0.87	140	empty
5	1067	0.86	0.87	142	empty

Interfaces

6 interfaces between chains.

B–C · 3278 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 3273 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 3267 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 3264 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 29 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

5T4D · Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703 · 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 0.99

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 Q13563
Elsewhere: RCSB PDB 5T4D · PDBe 5T4D · UniProt Q13563

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