MolNFT v1 · #78420 · protein
Crystal structure of a papaya latex serine protease inhibitor (ppi) at 2.6A resolution
3S8J · Latex serine proteinase inhibitor: “Crystal structure of a papaya latex serine protease inhibitor (ppi) at 2.6A resolution”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.77). MolNFT v1 #78420 on GenesisL1: 3D…
- PDB
- 3S8J
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Latex serine proteinase inhibitor
- UniProt
- P80691
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Latex serine proteinase inhibitor | protein | 182 | 3% helix, 39% strand | P80691 |
| B | Latex serine proteinase inhibitor | protein | 181 | 4% helix, 35% strand | P80691 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 565 | 0.77 | 0.84 | 53 | empty |
| 2 | 66 | 0.38 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 642 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3S8J · Crystal structure of a papaya latex serine protease inhibitor (PPI) at 2.6A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P80691 · AlphaFold monomer V2.0 prediction for latex serine proteinase inhibitor (P80691) · a predicted model of the same protein · chain B 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 P80691
- Elsewhere: RCSB PDB 3S8J · PDBe 3S8J · UniProt P80691
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