Research workbench
Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis
Analyse Insight into subtilisin E-S7 cleavage pattern based on crystal structure and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O44
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nattokinase
- EC
- 3.4.21.62
- UniProt
- A0A024B5N4
- Ligands
- CA, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nattokinase (EC 3.4.21.62) | protein | 276 | 30% helix, 20% strand | A0A024B5N4 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.62 | 0.78 | 38 | empty |
| 2 | 376 | 0.60 | 0.77 | 40 | EDO, CA |
| 3 | 88 | 0.38 | 0.76 | 28 | CA, EDO |
Interfaces
1 interface between chains.
- A–B · 246 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6O44 · Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates… · the same entry in another collection · 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 A0A024B5N4
- Elsewhere: RCSB PDB 6O44 · PDBe 6O44 · UniProt A0A024B5N4
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