Research workbench
Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5
Analyse Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JDT
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.68
- Source
- Aspergillus fumigatus Z5
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- A0A0J5Q413
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · resolution 1.68 · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 319 | 44% helix, 20% strand | A0A0J5Q413 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.47 | 0.78 | 27 | empty |
| 2 | 122 | 0.44 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 439 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6JDT · Crystal structure of GH10 family xylanase XYNAF1 from aspergillus fumigatus Z5 · the same entry in another collection · 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 A0A0J5Q413
- Elsewhere: RCSB PDB 6JDT · PDBe 6JDT · UniProt A0A0J5Q413
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