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Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues
Analyse Crystallographic analysis of transition-state mimics bound to penicillopepsin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PPM
- Type
- protein
- Length
- 323 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillopepsin
- EC
- 3.4.23.20
- UniProt
- P00798
- Ligands
- 0P1, MAN, ARA, SO4
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Penicillopepsin (EC 3.4.23.20) | protein | 323 | 14% helix, 48% strand | P00798 |
Ligands and binding sites
- 0P1 · N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl }-L-alaninamide · ligand · chains E
- MAN · alpha-D-mannopyranose · sugar · chains E
- ARA · alpha-L-arabinopyranose · sugar · chains E
- SO4 · Sulfate ion · ion · chains E
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 | 341 | 0.61 | 0.77 | 47 | 0P1 |
Modifications
Observed in the structure: 2 glycan, 1 disulfide (O-glycosylation, disulfide).
Compared structures
- 1PPM · Crystallographic analysis of transition-state mimics bound to penicillopepsin… · 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 1PPM · PDBe 1PPM · UniProt P00798
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