Research workbench
Binding of a reduced peptide inhibitor to the aspartic proteinase from rhizopus chinensis. implications for a mechanism of action
Analyse Binding of a reduced peptide inhibitor to the aspartic proteinase from rhizopus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3APR
- Type
- protein
- Length
- 329 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhizopuspepsin; Reduced peptide inhibitor
- EC
- 3.4.23.6
- UniProt
- P06026
- Ligands
- PUK
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Rhizopuspepsin (EC 3.4.23.6) | protein | 325 | 14% helix, 46% strand | P06026 |
| I | Reduced peptide inhibitor | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- PUK · N-[(2S)-2-amino-3-phenylpropyl]-L-phenylalanine · ligand · chains E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.60 | 0.87 | 27 | PUK |
| 2 | 51 | 0.32 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- E–I · 533 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 3APR · Binding of a reduced peptide inhibitor to the aspartic proteinase from rhizopus… · the same entry in another collection · chain E against E, TM-score 1.00
- P06026 · AlphaFold monomer V2.0 prediction for rhizopuspepsin (P06026) · a predicted model of the same protein · chain E against A, TM-score 1.00
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 P06026
- Elsewhere: RCSB PDB 3APR · PDBe 3APR · UniProt P06026
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