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Crystal structure of GH30 (mutant E188A) complexed with aldotriuronic acid from thermothelomyces thermophila.
Analyse Crystal structure of GH30 (mutant E188A) complexed with aldotriuronic acid from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O0E
- Type
- protein
- Length
- 893 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH30 family xylanase
- EC
- 3.2.1.-
- UniProt
- G2Q1N4
- Ligands
- GLY, GCV, XYP, NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | GH30 family xylanase (EC 3.2.1.-) | protein | 452 | 23% helix, 31% strand | G2Q1N4 |
| A | GH30 family xylanase (EC 3.2.1.-) | protein | 441 | 23% helix, 31% strand | G2Q1N4 |
Ligands and binding sites
- GLY · Glycine · ligand · 5 copies · chains G, A
- GCV · 4-O-methyl-alpha-D-glucopyranuronic acid · ligand · 2 copies · chains A, G
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains G
- EDO · 1,2-ethanediol · additive · 4 copies · chains G, A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.61 | 0.77 | 42 | EDO |
| 2 | 100 | 0.49 | 0.81 | 18 | XYP |
| 3 | 115 | 0.44 | 0.77 | 27 | XYP, GCV |
| 4 | 142 | 0.43 | 0.75 | 32 | empty |
| 5 | 89 | 0.33 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- G–A · 662 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7O0E · Crystal structure of GH30 (mutant E188A) complexed with aldotriuronic acid from… · the same entry in another collection · chain G against G, TM-score 1.00
- G2Q1N4 · AlphaFold monomer V2.0 prediction for GH30 family xylanase (G2Q1N4) · 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 G2Q1N4
- Elsewhere: RCSB PDB 7O0E · PDBe 7O0E · UniProt G2Q1N4
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