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Crystal structure of arabidopsis thaliana legumain isoform gamma in two-chain activation state
Analyse Crystal structure of arabidopsis thaliana legumain isoform gamma in two-chain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NIJ
- Type
- protein
- Length
- 1,710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar-processing enzyme gamma-isozyme
- EC
- 3.4.22.34
- UniProt
- Q39119
- Ligands
- SNN, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Vacuolar-processing enzyme gamma-isozyme (EC 3.4.22.34) | protein | 428 | 43% helix, 11% strand | Q39119 |
| B | Vacuolar-processing enzyme gamma-isozyme (EC 3.4.22.34) | protein | 427 | 42% helix, 11% strand | Q39119 |
| D | Vacuolar-processing enzyme gamma-isozyme (EC 3.4.22.34) | protein | 427 | 43% helix, 11% strand | Q39119 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.77 | 0.82 | 88 | SO4 |
| 2 | 581 | 0.76 | 0.82 | 85 | empty |
| 3 | 225 | 0.68 | 0.85 | 34 | CIT |
| 4 | 300 | 0.65 | 0.81 | 45 | empty |
| 5 | 244 | 0.65 | 0.83 | 37 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1306 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1209 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 442 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 covalent, 4 modified (disulfide, covalent ligand, methylation).
Compared structures
- 5NIJ · Crystal structure of arabidopsis thaliana legumain isoform gamma in two-chain activation… · the same entry in another collection · chain C against C, TM-score 1.00
- Q39119 · AlphaFold monomer V2.0 prediction for vacuolar-processing enzyme gamma-isozyme (Q39119) · 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 Q39119
- Elsewhere: RCSB PDB 5NIJ · PDBe 5NIJ · UniProt Q39119
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