Research workbench

Cryo-EM structure of PKD2 C331S disease variant

Analyse Cryo-EM structure of PKD2 C331S disease variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WB8
Type: protein
Length: 1,852 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 0.87

Structure

electron microscopy · 1 distinct chain · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Polycystin-2	protein	463	56% 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	321	0.87	0.97	33	empty
2	1041	0.86	0.87	131	empty
3	998	0.85	0.86	108	empty
4	952	0.85	0.86	98	empty
5	1199	0.84	0.85	129	empty

Interfaces

6 interfaces between chains.

A–C · 3222 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 3219 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 3218 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 3214 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 22 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6WB8 · Cryo-EM structure of PKD2 C331S disease variant · 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 6WB8 · PDBe 6WB8 · UniProt Q13563

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