Research workbench
P62/SQSTM1 zz domain with ile-peptide
Analyse P62/SQSTM1 zz domain with ile-peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YPH
- Type
- protein
- Length
- 100 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated PROTEIN,SEQUESTOSOME-1
- UniProt
- P11021, Q13501
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 78 kda glucose-regulated PROTEIN,SEQUESTOSOME-1 | protein | 51 | 10% helix, 27% strand | P11021, Q13501 |
| B | 78 kda glucose-regulated PROTEIN,SEQUESTOSOME-1 | protein | 49 | 10% helix, 24% strand | P11021, Q13501 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.35 | 0.77 | 13 | empty |
| 2 | 52 | 0.33 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5YPH · p62/SQSTM1 ZZ domain with Ile-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 B against A, TM-score 0.85
- P11021 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (P11021) · a predicted model of the same protein · chain B against A, TM-score 0.37
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 P11021
- Every structure of UniProt Q13501
- Elsewhere: RCSB PDB 5YPH · PDBe 5YPH · UniProt P11021 · UniProt Q13501
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