Research workbench
Xylooligosaccharide oxidase from myceliophthora thermophila C1 in complex with xylobiose
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
- 5L6F
- Type
- protein
- Length
- 473 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD linked oxidase-like protein
- EC
- 1.1.3.-
- UniProt
- G2QG48
- Ligands
- FAD, XYP, NAG
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 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
- XYP · beta-D-xylopyranose · sugar · 8 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 549 | 0.82 | 0.88 | 69 | XYP, FAD |
| 2 | 56 | 0.25 | 0.72 | 15 | empty |
Modifications
Observed in the structure: 5 glycan, 2 cofactor, 1 disulfide (N-glycosylation, flavinylation, disulfide).
Compared structures
- 5L6F · Xylooligosaccharide oxidase from Myceliophthora thermophila C1 in complex with Xylobiose · 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 5L6F · PDBe 5L6F · UniProt G2QG48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.