Research workbench
Melanocarpus albomyces laccase crystal soaked (10 sec) with 2,6- dimethoxyphenol
Analyse Melanocarpus albomyces laccase crystal soaked (10 sec) with 2,6- dimethoxyphenol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FU8
- Type
- protein
- Length
- 1,118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase-1
- EC
- 1.10.3.2
- UniProt
- Q70KY3
- Ligands
- 3DM, NAG, MAN, CU, SO4, CL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 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
- 3DM · 2,6-dimethoxyphenol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.85 | 0.89 | 91 | 3DM, GOL |
| 2 | 105 | 0.78 | 0.97 | 28 | empty |
| 3 | 100 | 0.78 | 0.98 | 24 | empty |
| 4 | 886 | 0.71 | 0.76 | 76 | NAG |
| 5 | 109 | 0.63 | 0.88 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 736 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 4 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard, glycosylation).
Compared structures
- 3FU8 · Melanocarpus albomyces laccase crystal soaked (10 sec) with 2,6-dimethoxyphenol · the same entry in another collection · chain B against B, TM-score 1.00
- Q70KY3 · AlphaFold monomer V2.0 prediction for laccase-1 (Q70KY3) · 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 Q70KY3
- Elsewhere: RCSB PDB 3FU8 · PDBe 3FU8 · UniProt Q70KY3
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