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Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4- glucanase from ruminal metagenomic library, in complex with xxlg
Analyse Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4- glucanase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W8B
- Type
- protein
- Length
- 386 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-xyloglucanase
- UniProt
- D2XML9
- Ligands
- BGC, XYS, GLC, GAL, SO4
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-xyloglucanase | protein | 386 | 45% helix, 13% strand | D2XML9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A
- XYS · alpha-D-xylopyranose · sugar · 5 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 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 | 329 | 0.55 | 0.75 | 45 | GLC, XYS |
| 2 | 68 | 0.41 | 0.80 | 20 | SO4 |
Compared structures
- 4W8B · Crystal structure of XEG5B, a GH5 xyloglucan-specific beta-1,4-glucanase from ruminal… · 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 D2XML9
- Elsewhere: RCSB PDB 4W8B · PDBe 4W8B · UniProt D2XML9
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