MolNFT v1 · #140876 · protein
P62/SQSTM1 zz domain with phe-peptide
5YPC · 78 kda glucose-regulated PROTEIN,SEQUESTOSOME-1: “P62/SQSTM1 zz domain with phe-peptide”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.41). MolNFT v1 #140876 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5YPC
- Type
- protein
- Length
- 199 residues
- Chains
- 4
- 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
- 4 · best druggability 0.41
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 | 49 | 10% helix, 24% strand | P11021, Q13501 |
| B, C, D | 78 kda glucose-regulated PROTEIN,SEQUESTOSOME-1 | protein | 50 | 10% helix, 28% strand | P11021, 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.41 | 0.80 | 15 | empty |
| 2 | 63 | 0.35 | 0.78 | 25 | empty |
| 3 | 54 | 0.32 | 0.77 | 19 | empty |
| 4 | 65 | 0.30 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–D · 795 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 447 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 431 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 220 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 103 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YPC · p62/SQSTM1 ZZ domain with Phe-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 A against A, TM-score 0.89
- P11021 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (P11021) · a predicted model of the same protein · chain A against A, TM-score 0.38
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 5YPC · PDBe 5YPC · UniProt P11021 · UniProt Q13501
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