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A new crystal structure of a Fusarium oxysporum GH10 xylanase reveals the presence of an extended loop on top of the catalytic cleft
Analyse A new crystal structure of a Fusarium oxysporum GH10 xylanase reveals the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U7B
- Type
- protein
- Length
- 1,632 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Fusarium oxysporum
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- Ligands
- NAG, BMA, MAN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.94 · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 327 | 41% helix, 20% strand | — |
| B, C, E | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 326 | 41% helix, 20% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B, C, D, E
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, D, E
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, D, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.81 | 0.83 | 97 | EDO |
| 2 | 853 | 0.81 | 0.84 | 95 | EDO |
| 3 | 388 | 0.80 | 0.89 | 40 | empty |
| 4 | 295 | 0.67 | 0.83 | 39 | empty |
| 5 | 126 | 0.56 | 0.83 | 24 | empty |
Interfaces
9 interfaces between chains.
- B–C · 833 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 827 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 558 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 376 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3U7B · A new crystal structure of a fusarium oxysporum GH10 xylanase reveals the presence of an… · 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
- Elsewhere: RCSB PDB 3U7B · PDBe 3U7B
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