Research workbench
Structure of the FAMILY43 beta-xylosidase D128G mutant from geobacillus stearothermophilus in complex with xylobiose
Analyse Structure of the FAMILY43 beta-xylosidase D128G mutant from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EXJ
- Type
- protein
- Length
- 2,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-xylosidase
- EC
- 3.2.1.37
- UniProt
- Q68HB3
- Ligands
- XYS, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-D-xylosidase (EC 3.2.1.37) | protein | 533 | 1% helix, 46% strand | Q68HB3 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.81 | 0.82 | 95 | XYS |
| 2 | 955 | 0.80 | 0.82 | 90 | XYS |
| 3 | 415 | 0.73 | 0.83 | 40 | empty |
| 4 | 419 | 0.72 | 0.83 | 40 | empty |
| 5 | 319 | 0.64 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2150 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2142 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 865 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 835 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2EXJ · Structure of the family43 beta-Xylosidase D128G mutant from geobacillus… · 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 Q68HB3
- Elsewhere: RCSB PDB 2EXJ · PDBe 2EXJ · UniProt Q68HB3
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