Research workbench
Crystal structure of the extracellular xylanase from geobacillus stearothermophilus T-6 (XT6, monoclinic form): the complex of the wt enzyme with xylopentaose at 1.67A resolution
Analyse Crystal structure of the extracellular xylanase from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R87
- Type
- protein
- Length
- 371 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- P40943
- Ligands
- XYP, ZN, CL, SO4
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 371 | 42% helix, 19% strand | P40943 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 5 copies · chains A
- ZN · Zinc ion · metal · 7 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.50 | 0.79 | 28 | XYP |
Compared structures
- 1R87 · Crystal structure of the extracellular xylanase from Geobacillus stearothermophilus T-6… · the same entry in another collection · chain A against A, TM-score 1.00
- P40943 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P40943) · a predicted model of the same protein · 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 P40943
- Elsewhere: RCSB PDB 1R87 · PDBe 1R87 · UniProt P40943
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