Research workbench

The crystal structure of PB1 homo-dimer of human P62/SQSTM1

Analyse The crystal structure of PB1 homo-dimer of human P62/SQSTM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JM4
Type: protein
Length: 322 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sequestosome-1
UniProt: Q13501
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sequestosome-1	protein	81	23% helix, 41% strand	Q13501
B	Sequestosome-1	protein	75	28% helix, 32% strand	Q13501
D	Sequestosome-1	protein	84	23% helix, 33% strand	Q13501
C	Sequestosome-1	protein	82	23% helix, 40% strand	Q13501

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.65	0.87	29	empty
2	232	0.49	0.75	34	empty
3	92	0.41	0.78	19	empty

Interfaces

5 interfaces between chains.

A–B · 540 Å² buried · 9 hydrogen bonds · protein-protein
D–C · 524 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 389 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 70 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6JM4 · The crystal structure of PB1 homo-dimer of human P62/SQSTM1 · the same entry in another collection · chain C against C, TM-score 1.00
Q13501 · AlphaFold monomer V2.0 prediction for sequestosome-1 (Q13501) · 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 Q13501
Elsewhere: RCSB PDB 6JM4 · PDBe 6JM4 · UniProt Q13501

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