Research workbench

p62/SQSTM1 ZZ domain with Gly-peptide

Analyse p62/SQSTM1 ZZ domain with Gly-peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KHZ
Type: protein
Length: 189 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Homo sapiens
Molecule: Sequestosome-1
UniProt: Q13501
Ligands: ZN
Pockets: 2 · best druggability 0.29

Structure

x-ray diffraction · resolution 2.8 · 3 distinct chains · 11% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sequestosome-1	protein	49	10% helix, 24% strand	Q13501
C	Sequestosome-1	protein	45	11% helix, 27% strand	Q13501
D	Sequestosome-1	protein	46	11% helix, 30% strand	Q13501

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	52	0.29	0.76	21	empty
2	59	0.29	0.74	15	empty

Interfaces

5 interfaces between chains.

B–D · 440 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 356 Å² buried · 1 hydrogen bond · protein-protein
B–C · 355 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 161 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 14 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6KHZ · P62/SQSTM1 zz domain with gly-peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q13501 · AlphaFold monomer V2.0 prediction for sequestosome-1 (Q13501) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 6KHZ · PDBe 6KHZ · UniProt Q13501

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