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Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant xylanase from streptomyces olivaceoviridis E-86
Analyse Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D22
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-D-xylanase
- EC
- 3.2.1.8
- UniProt
- Q7SI98
- Ligands
- XYS, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-D-xylanase (EC 3.2.1.8) | protein | 427 | 34% helix, 24% strand | Q7SI98 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.66 | 0.80 | 49 | empty |
| 2 | 128 | 0.38 | 0.73 | 22 | empty |
| 3 | 79 | 0.35 | 0.76 | 23 | XYS |
| 4 | 53 | 0.32 | 0.77 | 17 | XYS |
| 5 | 55 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1026 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, glycosylation).
Compared structures
- 2D22 · Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant… · 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 Q7SI98
- Elsewhere: RCSB PDB 2D22 · PDBe 2D22 · UniProt Q7SI98
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