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Cryoem structure of polycystin-2 in complex with calcium and lipids

Analyse Cryoem structure of polycystin-2 in complex with calcium and lipids in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MKF
Type: protein
Length: 1,924 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polycystin-2
UniProt: Q13563
Ligands: PLM, CHS, PX6, NAG, CA
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Polycystin-2	protein	481	53% helix, 10% strand	Q13563

Ligands and binding sites

PLM · Palmitic acid · ligand · 12 copies · chains A, B, C, D
CHS · 4-amino-5-cyclohexyl-3-hydroxy-pentanoic acid · ligand · 8 copies · chains A, B, C, D
PX6 · 1,2-dipalmitoyl-sn-glycero-3-phosphate · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
CA · Calcium ion · metal · 5 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	337	0.83	0.92	56	empty
2	336	0.83	0.92	55	empty
3	335	0.83	0.92	55	empty
4	335	0.83	0.92	57	empty
5	194	0.80	0.94	24	CA

Interfaces

6 interfaces between chains.

A–B · 3236 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 3206 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 3205 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 3202 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 27 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

5MKF · cryoEM Structure of Polycystin-2 in complex with calcium and lipids · the same entry in another collection · chain C against C, TM-score 1.00
Q13563 · AlphaFold monomer V2.0 prediction for polycystin-2 (Q13563) · a predicted model of the same protein · chain D 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 Q13563
Elsewhere: RCSB PDB 5MKF · PDBe 5MKF · UniProt Q13563

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