Research workbench
Beta-1,4-xylanase from chaetomium thermophilum complexed with methyl thioxylopentoside
Analyse Beta-1,4-xylanase from chaetomium thermophilum complexed with methyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XNK
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoxylanase 11A
- EC
- 3.2.1.8
- UniProt
- Q8J1V6
- Ligands
- TWY, Z4U, SO4
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoxylanase 11A (EC 3.2.1.8) | protein | 191 | 5% helix, 65% strand | Q8J1V6 |
Ligands and binding sites
- TWY · 4-thio-beta-D-xylopyranose · ligand · 4 copies · chains A, B
- Z4U · methyl 4-thio-alpha-D-xylopyranoside · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.54 | 0.77 | 34 | Z4U, TWY |
| 2 | 193 | 0.52 | 0.78 | 30 | Z4U, TWY |
Interfaces
1 interface between chains.
- A–B · 422 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cyclization).
Compared structures
- 1XNK · Beta-1,4-xylanase from Chaetomium thermophilum complexed with methyl thioxylopentoside · 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 Q8J1V6
- Elsewhere: RCSB PDB 1XNK · PDBe 1XNK · UniProt Q8J1V6
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