Research workbench
Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from gloeophyllum trabeum
Analyse Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XX6
- Type
- protein
- Length
- 639 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- S7Q6I2
- Ligands
- MAN, NAG, BMA, MG, UNX, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylanase (EC 3.2.1.8) | protein | 318 | 45% helix, 20% strand | S7Q6I2 |
| B | Beta-xylanase (EC 3.2.1.8) | protein | 321 | 44% helix, 21% strand | S7Q6I2 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 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 | 255 | 0.75 | 0.88 | 24 | P6G |
| 2 | 210 | 0.46 | 0.74 | 27 | empty |
| 3 | 135 | 0.43 | 0.76 | 22 | GOL |
| 4 | 149 | 0.43 | 0.75 | 30 | GOL |
Interfaces
1 interface between chains.
- A–B · 626 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 4XX6 · Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family… · 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 S7Q6I2
- Elsewhere: RCSB PDB 4XX6 · PDBe 4XX6 · UniProt S7Q6I2
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