Research workbench
Crystal structure of endo-1,4-beta-xylanase (NP_811807.1) from bacteroides thetaiotaomicron vpi-5482 at 1.70 a resolution
Analyse Crystal structure of endo-1,4-beta-xylanase (NP_811807.1) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KST
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- UniProt
- Q8A3Q9
- Ligands
- CA
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase | protein | 291 | 3% helix, 52% strand | Q8A3Q9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.60 | 0.78 | 28 | empty |
| 2 | 178 | 0.58 | 0.82 | 34 | empty |
| 3 | 282 | 0.58 | 0.77 | 24 | empty |
| 4 | 82 | 0.39 | 0.78 | 18 | EDO |
| 5 | 85 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 557 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3KST · Crystal structure of Endo-1,4-beta-xylanase (NP_811807.1) from BACTEROIDES… · 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 Q8A3Q9
- Elsewhere: RCSB PDB 3KST · PDBe 3KST · UniProt Q8A3Q9
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