Research workbench
Ligand complex structure of GH10 family xylanase XYNAF1, soaking for 80 minutes
Analyse Ligand complex structure of GH10 family xylanase XYNAF1, soaking for 80 minutes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JE2
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- A0A0J5Q413
- Ligands
- XYP, NAG
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 319 | 43% helix, 20% strand | A0A0J5Q413 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 8 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- PEG · Di(hydroxyethyl)ether · 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 | 148 | 0.48 | 0.78 | 33 | XYP, GOL |
| 2 | 113 | 0.43 | 0.77 | 25 | XYP, GOL |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6JE2 · Ligand complex structure of GH10 family xylanase XynAF1, soaking for 80 minutes · 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 6JE2 · PDBe 6JE2 · UniProt A0A0J5Q413
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