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Specificity and affnity of natural product cyclopentapeptide inhibitor argadin against aspergillus fumigatus chitinase
Analyse Specificity and affnity 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
- 1W9U
- Type
- protein
- Length
- 795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase; Argadin
- EC
- 3.2.1.14
- UniProt
- Q873X9
- Ligands
- HSE, UN1, SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase (EC 3.2.1.14) | protein | 395 | 37% helix, 20% strand | Q873X9 |
| B | Chitinase (EC 3.2.1.14) | protein | 394 | 38% helix, 20% strand | Q873X9 |
| C, D | Argadin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- HSE · L-homoserine · ligand · 2 copies · chains A, C, B, D
- UN1 · 2-aminohexanedioic acid · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.61 | 0.84 | 23 | UN1 |
| 2 | 133 | 0.60 | 0.85 | 18 | UN1 |
| 3 | 150 | 0.57 | 0.82 | 28 | HSE |
| 4 | 146 | 0.54 | 0.81 | 29 | HSE |
| 5 | 206 | 0.48 | 0.75 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–D · 448 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 429 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 404 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 2 d-amino, 2 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 1W9U · Specificity and affnity of natural product cyclopentapeptide inhibitor Argadin against… · the same entry in another collection · chain A against A, TM-score 1.00
- Q873X9 · AlphaFold monomer V2.0 prediction for endochitinase B1 (Q873X9) · a predicted model of the same protein · chain B 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 Q873X9
- Elsewhere: RCSB PDB 1W9U · PDBe 1W9U · UniProt Q873X9
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