Research workbench
Crystal structure of a surface pocket creating mutant (W6A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
Analyse Crystal structure of a surface pocket creating mutant (W6A) of an alkali… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EFD
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.674
- Source
- Bacillus sp. NG-27
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- O30700
- Ligands
- MG, NA, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.674 · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 354 | 45% helix, 17% strand | O30700 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.69 | 0.76 | 74 | EDO |
| 2 | 262 | 0.56 | 0.77 | 30 | EDO |
| 3 | 96 | 0.31 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 394 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5EFD · Crystal structure of a surface pocket creating mutant (W6A) of an alkali thermostable… · 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 O30700
- Elsewhere: RCSB PDB 5EFD · PDBe 5EFD · UniProt O30700
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.