Research workbench
Crystal structure determination of a blue laccase from lentinus tigrinus
Analyse Crystal structure determination of a blue laccase from lentinus tigrinus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QT6
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- Q5EBY5
- Ligands
- NAG, BMA, MAN, CU, CA, CL, PER
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Laccase (EC 1.10.3.2) | protein | 498 | 12% helix, 38% strand | Q5EBY5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PER · Peroxide ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.56 | 0.83 | 23 | GOL |
| 2 | 201 | 0.52 | 0.77 | 31 | CL |
| 3 | 131 | 0.52 | 0.80 | 21 | empty |
| 4 | 105 | 0.48 | 0.81 | 20 | empty |
| 5 | 107 | 0.47 | 0.80 | 22 | empty |
Modifications
Observed in the structure: 5 glycan, 4 disulfide (disulfide, N-glycosylation, glycosylation).
Compared structures
- 2QT6 · Crystal Structure Determination of a Blue Laccase from Lentinus Tigrinus · 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 Q5EBY5
- Elsewhere: RCSB PDB 2QT6 · PDBe 2QT6 · UniProt Q5EBY5
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