Research workbench
Crystal structure of glycoside hydrolase family 11 beta-xylanase from streptomyces olivaceoviridis E-86 in complex with alpha-L- arabinofuranosyl xylotetraose
Analyse Crystal structure of glycoside hydrolase family 11 beta-xylanase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DFN
- Type
- protein
- Length
- 771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- Ligands
- XYP, AHR, NA, CL
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 194 | 5% helix, 63% strand | — |
| C | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 193 | 5% helix, 65% strand | — |
| D | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 190 | 5% helix, 65% strand | — |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 12 copies · chains A, B, C
- AHR · alpha-L-arabinofuranose · sugar · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 59 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.67 | 0.83 | 57 | CL |
| 2 | 224 | 0.53 | 0.77 | 36 | XYP, CL |
| 3 | 205 | 0.52 | 0.77 | 30 | XYP, CL |
| 4 | 186 | 0.50 | 0.77 | 31 | XYP |
| 5 | 92 | 0.39 | 0.77 | 33 | CL |
Interfaces
4 interfaces between chains.
- C–D · 711 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 584 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 329 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 268 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7DFN · Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces… · 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 7DFN · PDBe 7DFN
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