Research workbench
Crystal structure of GH10 endo-B-1,4-xylanase (xynb) from xanthomonas axonopodis pv citri complexed with xylose
Analyse Crystal structure of GH10 endo-B-1,4-xylanase (xynb) from xanthomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PMY
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylanase
- UniProt
- Q8PET6
- Ligands
- XYP, CA
- Pockets
- 5 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylanase | protein | 303 | 40% helix, 15% strand | Q8PET6 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.41 | 0.75 | 26 | empty |
| 2 | 112 | 0.38 | 0.75 | 30 | empty |
| 3 | 70 | 0.38 | 0.78 | 15 | XYP, GOL |
| 4 | 68 | 0.35 | 0.77 | 15 | XYP, GOL |
| 5 | 84 | 0.34 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4PMY · Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri… · 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 Q8PET6
- Elsewhere: RCSB PDB 4PMY · PDBe 4PMY · UniProt Q8PET6
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