Research workbench
Crystal structure of GH10 xylanase from bispora. sp mey-1 with xylobiose
Analyse Crystal structure of GH10 xylanase from bispora. sp mey-1 with xylobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XZU
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- D0QF43
- Ligands
- NAG, BGC
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylanase (EC 3.2.1.8) | protein | 334 | 43% helix, 20% strand | D0QF43 |
| B | Beta-xylanase (EC 3.2.1.8) | protein | 333 | 44% helix, 20% strand | D0QF43 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.78 | 0.80 | 87 | NAG |
| 2 | 148 | 0.47 | 0.77 | 32 | BGC |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5XZU · Crystal structure of GH10 xylanase from Bispora. sp MEY-1 with xylobiose · 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 D0QF43
- Elsewhere: RCSB PDB 5XZU · PDBe 5XZU · UniProt D0QF43
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