MolNFT v2 · #72160 · protein
The Bowman-Birk type inhibitor from mung bean in ternary complex with porcine trypsin
3MYW: “The Bowman-Birk type inhibitor from mung bean in ternary complex with porcine trypsin”. X-ray diffraction at 2.5, 1 ligand (CA), 3 pockets (best druggability 0.57). MolNFT v2 #72160 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3MYW
- Type
- protein
- Length
- 501 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Sus scrofa; Vigna radiata var. radiata
- Molecule
- Trypsin; Bowman-Birk type trypsin inhibitor
- EC
- 3.4.21.4
- UniProt
- P00761, P01062
- Ligands
- CA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trypsin (EC 3.4.21.4) | protein | 223 | 11% helix, 35% strand | P00761 |
| I | Bowman-Birk type trypsin inhibitor | protein | 55 | 0% helix, 33% strand | P01062 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.57 | 0.83 | 30 | empty |
| 2 | 107 | 0.35 | 0.73 | 24 | empty |
| 3 | 93 | 0.33 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–I · 790 Ų buried · 22 hydrogen bonds · protein-protein
- I–B · 722 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 171 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 3MYW · The bowman-birk type inhibitor from mung bean in ternary complex with porcine trypsin · the same entry in another collection · chain A against A, TM-score 1.00
- P00761 · AlphaFold monomer V2.0 prediction for trypsin (P00761) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P01062 · AlphaFold monomer V2.0 prediction for bowman-birk type trypsin inhibitor (P01062) · a predicted model of the same protein · chain I against A, TM-score 0.87
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 P00761
- Every structure of UniProt P01062
- Elsewhere: RCSB PDB 3MYW · PDBe 3MYW · UniProt P00761 · UniProt P01062
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