MolNFT v1 · #36781 · protein
Crystal structure of presequence protease prep from arabidopsis thaliana
2FGE · Zinc metalloprotease (insulinase family): “Crystal structure of presequence protease prep from arabidopsis thaliana”. X-ray diffraction, 3 ligands (MG, ZN, CL), 20 pockets (best druggability 0.80). MolNFT v1 #36781 on GenesisL1: 3D…
- PDB
- 2FGE
- Type
- protein
- Length
- 1,970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc metalloprotease (insulinase family); Nonspecific peptide aaltra
- UniProt
- Q9LJL3
- Ligands
- MG, ZN, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Zinc metalloprotease (insulinase family) | protein | 979 | 50% helix, 19% strand | Q9LJL3 |
| D, E | Nonspecific peptide aaltra | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, E
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.80 | 0.85 | 51 | empty |
| 2 | 891 | 0.79 | 0.82 | 92 | empty |
| 3 | 644 | 0.73 | 0.80 | 68 | empty |
| 4 | 593 | 0.73 | 0.80 | 70 | empty |
| 5 | 1081 | 0.72 | 0.76 | 100 | MG |
Interfaces
3 interfaces between chains.
- A–B · 883 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 562 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 543 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 2FGE · Crystal structure of presequence protease PreP from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LJL3 · AlphaFold monomer V2.0 prediction for presequence protease 1, CHLOROPLASTIC/MITOCHONDRIAL… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9LJL3
- Elsewhere: RCSB PDB 2FGE · PDBe 2FGE · UniProt Q9LJL3
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