Research workbench
Na+-dependent allostery mediates coagulation factor protease active site selectivity
Analyse Na+-dependent allostery mediates coagulation factor protease active site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BEU
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin
- EC
- 3.4.21.4
- UniProt
- P00775
- Ligands
- BEN, NA, CA, SO4
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trypsin (EC 3.4.21.4) | protein | 224 | 13% helix, 37% strand | P00775 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.80 | 0.82 | 103 | SO4, BEN |
Interfaces
1 interface between chains.
- A–B · 668 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3BEU · Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity · the same entry in another collection · chain A against A, TM-score 1.00
- P00775 · AlphaFold monomer V2.0 prediction for trypsin (P00775) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00775
- Elsewhere: RCSB PDB 3BEU · PDBe 3BEU · UniProt P00775
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