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Specificity and affinity of natural product cyclopentapeptide inhibitor argadin against human chitinase
Analyse Specificity and affinity of natural product cyclopentapeptide inhibitor argadin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WAW
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitotriosidase 1; Argadin
- EC
- 3.2.1.14
- UniProt
- Q13231
- Ligands
- HSE, UN1, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitotriosidase 1 (EC 3.2.1.14) | protein | 365 | 36% helix, 24% strand | Q13231 |
| B | Argadin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- HSE · L-homoserine · ligand · chains A, B
- UN1 · 2-aminohexanedioic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion
- GOL · Glycerol · additive · 3 copies · chains A, B
- IPA · Isopropyl alcohol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.63 | 0.86 | 21 | UN1, GOL |
| 2 | 161 | 0.52 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 477 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 disulfide, 1 d-amino, 1 modified (covalent ligand, disulfide, D-amino acid, nonstandard).
Compared structures
- 1WAW · Specificity and affinity of natural product cyclopentapeptide inhibitor Argadin against… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13231 · AlphaFold monomer V2.0 prediction for chitotriosidase-1 (Q13231) · a predicted model of the same protein · 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 Q13231
- Elsewhere: RCSB PDB 1WAW · PDBe 1WAW · UniProt Q13231
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