Research workbench
Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 ångströms resolution
Analyse Crystallographic analysis of a pepstatin analogue binding to the aspartyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1APU
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (penicillopepsin); Pepstatin analogue isovaleryl-val-val-sta-O-et
- EC
- 3.4.23.20
- UniProt
- P00798
- Ligands
- IVA, MAN
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Protein (penicillopepsin) (EC 3.4.23.20) | protein | 323 | 13% helix, 48% strand | P00798 |
| I | Pepstatin analogue isovaleryl-val-val-sta-O-et | protein | 3 | 0% helix, 33% strand | — |
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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.32 | 0.73 | 22 | IVA |
Interfaces
1 interface between chains.
- E–I · 449 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 glycan, 1 modified (covalent ligand, disulfide, O-glycosylation, nonstandard).
Compared structures
- 1APU · Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase… · the same entry in another collection · chain E against E, TM-score 1.00
- P00798 · AlphaFold monomer V2.0 prediction for penicillopepsin-1 (P00798) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P00798
- Elsewhere: RCSB PDB 1APU · PDBe 1APU · UniProt P00798
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