Research workbench
Xylooligosaccharide oxidase from Myceliophthora thermophila C1 in complex with Xylose
Analyse Xylooligosaccharide oxidase from Myceliophthora thermophila C1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L6G
- Type
- protein
- Length
- 473 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.79
- Source
- Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)
- Molecule
- FAD linked oxidase-like protein
- EC
- 1.1.3.-
- UniProt
- G2QG48
- Ligands
- FAD, NAG, XYP, XYS
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.79 · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD linked oxidase-like protein (EC 1.1.3.-) | protein | 473 | 36% helix, 22% strand | G2QG48 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- XYP · beta-D-xylopyranose · sugar · 3 copies · chains A
- XYS · alpha-D-xylopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.81 | 0.87 | 67 | FAD, XYP |
| 2 | 60 | 0.26 | 0.73 | 16 | XYP |
Modifications
Observed in the structure: 5 glycan, 2 cofactor, 1 disulfide (N-glycosylation, flavinylation, disulfide).
Compared structures
- 5L6G · Xylooligosaccharide oxidase from myceliophthora thermophila C1 in complex with xylose · the same entry in another collection · chain A against A, TM-score 1.00
- G2QG48 · AlphaFold monomer V2.0 prediction for xylooligosaccharide oxidase (G2QG48) · 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 G2QG48
- Elsewhere: RCSB PDB 5L6G · PDBe 5L6G · UniProt G2QG48
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