Research workbench
Specificity and affinity of natural product cyclopentapeptide inhibitors against aspergillus fumigatus, human and bacterial chitinasefra
Analyse Specificity and affinity of natural product cyclopentapeptide inhibitors… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W9P
- Type
- protein
- Length
- 789 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase
- EC
- 3.2.1.14
- UniProt
- Q873X9
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% 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 | 39% helix, 20% strand | Q873X9 |
Ligands and binding sites
- 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.63 | 0.81 | 35 | empty |
| 2 | 268 | 0.63 | 0.80 | 34 | empty |
| 3 | 232 | 0.50 | 0.75 | 37 | empty |
| 4 | 52 | 0.33 | 0.78 | 19 | empty |
| 5 | 55 | 0.31 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 416 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1W9P · Specificity and affinity of natural product cyclopentapeptide inhibitors 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 1W9P · PDBe 1W9P · UniProt Q873X9
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