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Crystal structure of a fully functional laccase from the ligninolytic fungus pycnoporus cinnabarinus
Analyse Crystal structure of a fully functional laccase from the ligninolytic fungus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XYB
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- Q9UVQ2
- Ligands
- AS8, NAG, BMA, MAN, ZN, CU, NA, SO4, PER
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase (EC 1.10.3.2) | protein | 497 | 11% helix, 38% strand | Q9UVQ2 |
Ligands and binding sites
- AS8 · Acetylsulfate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · 8 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- PER · Peroxide ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- ACT · Acetate ion · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.50 | 0.81 | 25 | GOL |
| 2 | 179 | 0.49 | 0.77 | 33 | ACT, ZN |
| 3 | 117 | 0.45 | 0.78 | 22 | empty |
| 4 | 151 | 0.43 | 0.74 | 23 | empty |
| 5 | 50 | 0.32 | 0.78 | 15 | GOL |
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 2XYB · Crystal structure of a fully functional laccase from the ligninolytic fungus pycnoporus… · 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 Q9UVQ2
- Elsewhere: RCSB PDB 2XYB · PDBe 2XYB · UniProt Q9UVQ2
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