MolNFT v1 · #66995 · protein
Crystal structure of the plant subtilisin-like protease SBT3 in complex with a chloromethylketone inhibitor
3I74: “Crystal structure of the plant subtilisin-like protease SBT3 in complex with a chloromethylketone inhibitor”. X-ray diffraction, 4 ligands (ACE, NAG, FUC), 15 pockets (best druggability 0.62). MolNFT v1 #66995 on GenesisL1: 3D…
- PDB
- 3I74
- Type
- protein
- Length
- 1,290 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin-like protease; ACE-phe-glu-lys-ala chloromethylketone inhibitor
- UniProt
- O82777
- Ligands
- ACE, NAG, FUC, 0QE
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subtilisin-like protease | protein | 642 | 22% helix, 29% strand | O82777 |
| B | Subtilisin-like protease | protein | 640 | 23% helix, 29% strand | O82777 |
| C, D | ACE-phe-glu-lys-ala chloromethylketone inhibitor | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies
- 0QE · Chloromethane · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.62 | 0.78 | 28 | empty |
| 2 | 331 | 0.62 | 0.78 | 27 | empty |
| 3 | 348 | 0.60 | 0.77 | 31 | empty |
| 4 | 179 | 0.47 | 0.76 | 48 | empty |
| 5 | 158 | 0.43 | 0.75 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1246 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 389 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 377 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan, 2 covalent, 2 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
- 3I74 · Crystal Structure of the plant subtilisin-like protease SBT3 in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- O82777 · AlphaFold monomer V2.0 prediction for subtilisin-like protease SBT3 (O82777) · 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 O82777
- Elsewhere: RCSB PDB 3I74 · PDBe 3I74 · UniProt O82777
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