MolNFT v1 · #6125 · protein
Crystal structure of ascaris pepsin inhibitor-3 bound to porcine pepsin
1F34 · Pepsin a: “Crystal structure of ascaris pepsin inhibitor-3 bound to porcine pepsin”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #6125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1F34
- Type
- protein
- Length
- 464 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pepsin a; Major pepsin inhibitor pi-3
- EC
- 3.4.23.1
- UniProt
- P00791, P19400
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pepsin a (EC 3.4.23.1) | protein | 326 | 14% helix, 46% strand | P00791 |
| B | Major pepsin inhibitor pi-3 | protein | 138 | 36% helix, 27% strand | P19400 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.72 | 0.79 | 66 | MPD |
| 2 | 271 | 0.64 | 0.81 | 35 | empty |
| 3 | 138 | 0.50 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1652 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 modified (disulfide, phosphorylation).
Compared structures
- 1F34 · Crystal structure of ascaris pepsin inhibitor-3 bound to porcine pepsin · the same entry in another collection · chain A against A, TM-score 1.00
- P19400 · AlphaFold monomer V2.0 prediction for major pepsin inhibitor 3 (P19400) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P00791 · AlphaFold monomer V2.0 prediction for pepsin a (P00791) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P00791
- Every structure of UniProt P19400
- Elsewhere: RCSB PDB 1F34 · PDBe 1F34 · UniProt P00791 · UniProt P19400
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