Research workbench
Crystal structure of native xylanase 10B from thermotoga petrophila rku-1
Analyse Crystal structure of native xylanase 10B from thermotoga petrophila rku-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NIY
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- A5IL00
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 326 | 44% helix, 20% strand | A5IL00 |
| B | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 325 | 44% helix, 20% strand | A5IL00 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.54 | 0.75 | 40 | empty |
| 2 | 108 | 0.44 | 0.78 | 19 | ACT |
| 3 | 92 | 0.38 | 0.76 | 19 | ACT |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3NIY · Crystal structure of native xylanase 10B from Thermotoga petrophila RKU-1 · 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 A5IL00
- Elsewhere: RCSB PDB 3NIY · PDBe 3NIY · UniProt A5IL00
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.