MolNFT v1 · #1055 · protein
Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine-and difluorostatone-containing peptides
1APW: “Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine-and…”. X-ray diffraction, 5 ligands (IVA, NME, HSY), 2 pockets (best druggability 0.33). MolNFT v1 #1055 on GenesisL1: 3D structure…
- PDB
- 1APW
- Type
- protein
- Length
- 326 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillopepsin; Inhibitor isovaleryl (iva)-val-val-difluorostatine-N- methylamine
- EC
- 3.4.23.20
- UniProt
- P00798
- Ligands
- IVA, NME, HSY, MAN, SO4
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 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 |
| I | Inhibitor isovaleryl (iva)-val-val-difluorostatine-N- methylamine | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · chains E, I
- NME · Methylamine · ligand · chains E, I
- HSY · alpha-L-xylopyranose · ligand · chains E
- MAN · alpha-D-mannopyranose · sugar · chains E
- SO4 · Sulfate ion · ion · chains E
- DMF · Dimethylformamide · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.33 | 0.73 | 21 | IVA |
| 2 | 56 | 0.28 | 0.74 | 18 | NME, DMF |
Interfaces
1 interface between chains.
- E–I · 422 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 disulfide, 1 glycan, 1 modified (covalent ligand, disulfide, O-glycosylation, nonstandard).
Compared structures
- 1APW · 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 1APW · PDBe 1APW · UniProt P00798
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