MolNFT v1 · #25930 · protein
Specificity and affinity of natural product cyclopentapeptide argifin against aspergillus fumigatus
1W9V · Chitinase: “Specificity and affinity of natural product cyclopentapeptide argifin against aspergillus fumigatus”. X-ray diffraction, 3 ligands (IAS, DAL, SO4), 7 pockets (best druggability 0.60). MolNFT v1 #25930 on GenesisL1: 3D…
- PDB
- 1W9V
- Type
- protein
- Length
- 795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase; Argifin
- EC
- 3.2.1.14
- UniProt
- Q873X9
- Ligands
- IAS, DAL, SO4
- Pockets
- 7 · best druggability 0.60
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 | Argifin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- IAS · Beta-L-aspartic acid · ligand · 2 copies · chains A, C, B, D
- DAL · D-alanine · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.60 | 0.81 | 34 | DAL |
| 2 | 175 | 0.59 | 0.82 | 32 | DAL |
| 3 | 85 | 0.51 | 0.83 | 13 | empty |
| 4 | 210 | 0.48 | 0.75 | 30 | empty |
| 5 | 84 | 0.46 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 423 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 391 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 388 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 covalent (nonstandard, covalent ligand).
Compared structures
- 1W9V · Specificity and affinity of natural product cyclopentapeptide argifin against Aspergillus… · 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 1W9V · PDBe 1W9V · UniProt Q873X9
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