MolNFT v1 · #146838 · protein

Human polycsytin 2-L1

6DU8 · Polycystic kidney disease 2-like 1 protein: “Human polycsytin 2-L1”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.79). MolNFT v1 #146838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DU8
Type: protein
Length: 1,684 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polycystic kidney disease 2-like 1 protein
UniProt: Q9P0L9
Ligands: NAG
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 43% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Polycystic kidney disease 2-like 1 protein	protein	421	43% helix, 10% strand	Q9P0L9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 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	333	0.79	0.90	53	empty
2	371	0.78	0.88	54	empty
3	146	0.77	0.94	30	empty
4	157	0.76	0.93	29	empty
5	592	0.73	0.79	61	empty

Interfaces

6 interfaces between chains.

A–C · 2846 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2843 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 2841 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 2840 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 16 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6DU8 · Human Polycsytin 2-l1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9P0L9 · AlphaFold monomer V2.0 prediction for polycystic kidney disease 2-like 1 protein (Q9P0L9) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9P0L9
Elsewhere: RCSB PDB 6DU8 · PDBe 6DU8 · UniProt Q9P0L9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.