MolNFT v1 · #66983 · protein
Crystal structure of the plant subtilisin-like protease SBT3
3I6S: “Crystal structure of the plant subtilisin-like protease SBT3”. X-ray diffraction, 2 ligands (NAG, FUC), 12 pockets (best druggability 0.63). MolNFT v1 #66983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3I6S
- Type
- protein
- Length
- 1,281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin-like protease
- UniProt
- O82777
- Ligands
- NAG, FUC
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subtilisin-like protease | protein | 642 | 23% helix, 30% strand | O82777 |
| B | Subtilisin-like protease | protein | 639 | 23% helix, 29% strand | O82777 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.63 | 0.78 | 28 | empty |
| 2 | 455 | 0.62 | 0.76 | 45 | empty |
| 3 | 335 | 0.62 | 0.78 | 28 | empty |
| 4 | 72 | 0.40 | 0.79 | 17 | empty |
| 5 | 59 | 0.40 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1248 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3I6S · Crystal Structure of the plant subtilisin-like protease SBT3 · 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 3I6S · PDBe 3I6S · UniProt O82777
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