Research workbench
Crystal structure of aspergilloglutamic peptidase from aspergillus niger
Analyse Crystal structure of aspergilloglutamic peptidase from aspergillus niger in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y43
- Type
- protein
- Length
- 203 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspergillopepsin II light chain; Aspergillopepsin II heavy chain
- EC
- 3.4.23.19
- UniProt
- P24665
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspergillopepsin II light chain (EC 3.4.23.19) | protein | 32 | 0% helix, 63% strand | P24665 |
| B | Aspergillopepsin II heavy chain (EC 3.4.23.19) | protein | 171 | 0% helix, 63% strand | P24665 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.41 | 0.75 | 20 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2493 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1Y43 · crystal structure of aspergilloglutamic peptidase from Aspergillus niger · the same entry in another collection · chain A against A, TM-score 1.00
- P24665 · AlphaFold monomer V2.0 prediction for aspergillopepsin-2 (P24665) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P24665
- Elsewhere: RCSB PDB 1Y43 · PDBe 1Y43 · UniProt P24665
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