MolNFT v2 · #28128 · protein
Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59R/E60S mutant
1Y4A: “Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59R/E60S mutant”. X-ray diffraction at 1.6, 2 ligands (CA, NA), 2 pockets (best druggability 0.62). MolNFT v2 #28128 on GenesisL1: 3D structure…
- PDB
- 1Y4A
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Bacillus amyloliquefaciens; Hordeum vulgare
- Molecule
- subtilisin BPN'; chymotrypsin inhibitor 2
- EC
- 3.4.21.62
- UniProt
- P00782, Q40059
- Ligands
- CA, NA
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | subtilisin BPN' (EC 3.4.21.62) | protein | 275 | 30% helix, 22% strand | P00782 |
| I | chymotrypsin inhibitor 2 | protein | 63 | 22% helix, 35% strand | Q40059 |
Ligands and binding sites
- CA · Calcium ion · metal · chains E
- NA · Sodium ion · metal · chains E
- 15P · Polyethylene glycol (N=34) · additive · 2 copies · chains E
- CIT · Citric acid · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.62 | 0.88 | 24 | empty |
| 2 | 83 | 0.42 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- E–I · 925 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1Y4A · Crystal structure of the complex of subtilisin bpn' with chymotrypsin inhibitor 2… · the same entry in another collection · chain E against E, TM-score 1.00
- P00782 · AlphaFold monomer V2.0 prediction for subtilisin bpn' (P00782) · a predicted model of the same protein · chain E 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 P00782
- Every structure of UniProt Q40059
- Elsewhere: RCSB PDB 1Y4A · PDBe 1Y4A · UniProt P00782 · UniProt Q40059
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