Research workbench
Gamma-chymotrypsin D-naphthyl-1-acetamido boronic acid inhibitor complex
Analyse Gamma-chymotrypsin D-naphthyl-1-acetamido boronic acid inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4VGC
- Type
- protein
- Length
- 236 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma chymotrypsin
- EC
- 3.4.21.1
- UniProt
- P00766
- Ligands
- SRD, SO4
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma chymotrypsin (EC 3.4.21.1) | protein | 10 | 0% helix, 0% strand | P00766 |
| B | Gamma chymotrypsin (EC 3.4.21.1) | protein | 131 | 2% helix, 38% strand | P00766 |
| C | Gamma chymotrypsin (EC 3.4.21.1) | protein | 95 | 25% helix, 38% strand | P00766 |
Ligands and binding sites
- SRD · D-1-naphthyl-2-acetamido-ethane boronic acid · ligand · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.38 | 0.79 | 17 | SRD |
Interfaces
3 interfaces between chains.
- B–C · 2919 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 474 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 243 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4VGC · Gamma-chymotrypsin D-naphthyl-1-acetamido boronic acid inhibitor complex · the same entry in another collection · chain A against A, TM-score 1.00
- P00766 · AlphaFold monomer V2.0 prediction for chymotrypsinogen a (P00766) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P00766
- Elsewhere: RCSB PDB 4VGC · PDBe 4VGC · UniProt P00766
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