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Near-atomic resolution structure of a Melanocarpus albomyces laccase
Analyse Near-atomic resolution structure of a Melanocarpus albomyces laccase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q9O
- Type
- protein
- Length
- 1,118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.3
- Source
- Melanocarpus albomyces
- Molecule
- Laccase-1
- EC
- 1.10.3.2
- UniProt
- Q70KY3
- Ligands
- NAG, MAN, CU, SO4, CL, OXY
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · resolution 1.3 · 1 distinct chain · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Laccase-1 (EC 1.10.3.2) | protein | 559 | 13% helix, 38% strand | Q70KY3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.87 | 0.91 | 67 | GOL |
| 2 | 102 | 0.78 | 0.98 | 28 | empty |
| 3 | 98 | 0.78 | 0.98 | 24 | empty |
| 4 | 815 | 0.70 | 0.76 | 70 | NAG |
| 5 | 61 | 0.60 | 0.91 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
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 Q70KY3
- Elsewhere: RCSB PDB 2Q9O · PDBe 2Q9O · UniProt Q70KY3
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