Research workbench
Crystal structure of the bacillus circulans endo-beta-(1,4)-xylanase (bcx) N35E mutant with GLU78 covalently bonded to 2-deoxy-2-fluoro- xylobiose
Analyse Crystal structure of the bacillus circulans endo-beta-(1,4)-xylanase (bcx) N35E… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZN
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- P09850
- Ligands
- DFX, XYP, SO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 185 | 5% helix, 64% strand | P09850 |
Ligands and binding sites
- DFX · 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol · ligand · 2 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains B, 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 | 789 | 0.72 | 0.78 | 69 | DFX, XYP, SO4 |
| 2 | 51 | 0.41 | 0.83 | 16 | DFX, XYP |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3VZN · Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- P09850 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P09850) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P09850
- Elsewhere: RCSB PDB 3VZN · PDBe 3VZN · UniProt P09850
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