Research workbench
A psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase
Analyse A psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4Y
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylanase
- Ligands
- XYP
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylanase | protein | 314 | 43% helix, 17% strand | — |
| B | Xylanase | protein | 312 | 42% helix, 19% strand | — |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.50 | 0.78 | 30 | XYP |
| 2 | 136 | 0.41 | 0.74 | 21 | empty |
| 3 | 104 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 221 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D4Y · A psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase · 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
- Elsewhere: RCSB PDB 5D4Y · PDBe 5D4Y
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