Research workbench
Mesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor (APLP2)
Analyse Mesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JBT
- Type
- protein
- Length
- 276 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PRSS3 protein; Amyloid-like protein 2
- UniProt
- Q8N2U3, Q06481
- Ligands
- CA, SO4
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PRSS3 protein | protein | 224 | 11% helix, 36% strand | Q8N2U3 |
| X | Amyloid-like protein 2 | protein | 14 | 0% helix, 14% strand | Q06481 |
| Y | Amyloid-like protein 2 | protein | 38 | 26% helix, 29% strand | Q06481 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.57 | 0.79 | 41 | SO4 |
Interfaces
3 interfaces between chains.
- X–Y · 693 Ų buried · 10 hydrogen bonds · protein-protein
- A–Y · 633 Ų buried · 13 hydrogen bonds · protein-protein
- A–X · 372 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JBT · Mesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor (APLP2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q06481 · AlphaFold monomer V2.0 prediction for amyloid-like protein 2 (Q06481) · a predicted model of the same protein · chain Y against A, TM-score 0.43
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 Q8N2U3
- Every structure of UniProt Q06481
- Elsewhere: RCSB PDB 5JBT · PDBe 5JBT · UniProt Q8N2U3 · UniProt Q06481
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