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Crystal structure of michaelis complex of xylanase mutant (T82A, N127S, and E128H) from streptomyces olivaceoviridis E-86
Analyse Crystal structure of michaelis complex of xylanase mutant (T82A, N127S, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GQE
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- Q7SI98
- Ligands
- XYP
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 429 | 33% helix, 24% strand | Q7SI98 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.66 | 0.80 | 48 | empty |
| 2 | 102 | 0.43 | 0.77 | 26 | empty |
| 3 | 92 | 0.38 | 0.76 | 19 | XYP |
| 4 | 74 | 0.34 | 0.76 | 17 | XYP |
| 5 | 77 | 0.32 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1032 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5GQE · Crystal structure of michaelis complex of xylanase mutant (T82A, N127S, and E128H) from… · 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 5GQE · PDBe 5GQE · UniProt Q7SI98
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