Research workbench
Crystal structure of the bacillus circulans endo-beta-(1,4)-xylanase (bcx) N35H mutant
Analyse Crystal structure of the bacillus circulans endo-beta-(1,4)-xylanase (bcx) N35H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZL
- Type
- protein
- Length
- 740 residues
- Chains
- 4
- 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
- SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 185 | 5% helix, 64% strand | P09850 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.82 | 0.83 | 117 | empty |
| 2 | 118 | 0.43 | 0.77 | 25 | empty |
| 3 | 78 | 0.42 | 0.80 | 21 | empty |
| 4 | 68 | 0.29 | 0.74 | 26 | empty |
| 5 | 51 | 0.27 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 791 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 218 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 159 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 135 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3VZL · Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H 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 3VZL · PDBe 3VZL · UniProt P09850
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