Research workbench
Crystal structure of xylanase from streptomyces olivaceoviridis E-86 complexed with lactose
Analyse Crystal structure of xylanase from streptomyces olivaceoviridis E-86 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IT0
- 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
- GAL, BGC
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-D-xylanase (EC 3.2.1.8) | protein | 427 | 33% helix, 25% strand | Q7SI98 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.66 | 0.80 | 47 | empty |
| 2 | 78 | 0.33 | 0.75 | 18 | empty |
| 3 | 62 | 0.33 | 0.77 | 17 | empty |
| 4 | 58 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1048 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1IT0 · Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with… · 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 1IT0 · PDBe 1IT0 · UniProt Q7SI98
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