MolNFT v1 · #19226 · protein
Crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase.
1QDM: “Crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase.”. X-ray diffraction, 17 pockets (best druggability 0.75). MolNFT v1 #19226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1QDM
- Type
- protein
- Length
- 1,287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prophytepsin
- EC
- 3.4.23.40
- UniProt
- P42210
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prophytepsin (EC 3.4.23.40) | protein | 430 | 28% helix, 34% strand | P42210 |
| C | Prophytepsin (EC 3.4.23.40) | protein | 427 | 27% helix, 33% strand | P42210 |
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.75 | 0.79 | 77 | empty |
| 2 | 57 | 0.70 | 0.97 | 21 | empty |
| 3 | 346 | 0.70 | 0.83 | 46 | empty |
| 4 | 318 | 0.63 | 0.80 | 36 | empty |
| 5 | 259 | 0.57 | 0.78 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 788 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1QDM · Crystal structure of prophytepsin, a zymogen of a barley vacuolar aspartic proteinase. · the same entry in another collection · chain A against A, TM-score 1.00
- P42210 · AlphaFold monomer V2.0 prediction for phytepsin (P42210) · a predicted model of the same protein · chain A 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 P42210
- Elsewhere: RCSB PDB 1QDM · PDBe 1QDM · UniProt P42210
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