MolNFT v1 · #145914 · protein

Human PKD2 F604P mutant

6D1W · Polycystin-2: “Human PKD2 F604P mutant”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.89). MolNFT v1 #145914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D1W
Type: protein
Length: 1,804 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 0.89

Structure

electron microscopy · 1 distinct chain · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Polycystin-2	protein	451	54% helix, 12% 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	1032	0.89	0.90	96	empty
2	1015	0.86	0.86	105	empty
3	977	0.86	0.87	113	empty
4	1043	0.86	0.86	117	empty
5	1124	0.84	0.85	117	empty

Interfaces

4 interfaces between chains.

B–D · 2990 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 2978 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 2977 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 2976 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6D1W · human PKD2 F604P mutant · 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 6D1W · PDBe 6D1W · UniProt Q13563

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