Research workbench
GH10 endo-xylanase in complex with xylobiose epoxide inhibitor
Analyse GH10 endo-xylanase in complex with xylobiose epoxide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q8N
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- A0A1L9WG58
- Ligands
- HQ8, NAG, XYP, K
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 321 | 45% helix, 20% strand | A0A1L9WG58 |
Ligands and binding sites
- HQ8 · (1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 26 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 | 201 | 0.51 | 0.77 | 33 | EDO, HQ8, XYP |
| 2 | 53 | 0.49 | 0.86 | 14 | EDO |
| 3 | 155 | 0.48 | 0.77 | 30 | EDO, HQ8, XYP |
| 4 | 112 | 0.40 | 0.76 | 19 | EDO |
| 5 | 59 | 0.32 | 0.77 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6Q8N · GH10 endo-xylanase in complex with xylobiose epoxide inhibitor · 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 A0A1L9WG58
- Elsewhere: RCSB PDB 6Q8N · PDBe 6Q8N · UniProt A0A1L9WG58
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