Research workbench
Crystal structure of laccase from lentinus sp. at 1.8 a resolution
Analyse Crystal structure of laccase from lentinus sp. at 1.8 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X1B
- Type
- protein
- Length
- 1,000 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- Ligands
- MAN, NAG, BMA, CU
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Laccase (EC 1.10.3.2) | protein | 500 | 11% helix, 39% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- CU · Copper (II) ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.83 | 0.83 | 111 | empty |
| 2 | 481 | 0.70 | 0.80 | 70 | empty |
| 3 | 257 | 0.54 | 0.76 | 42 | empty |
| 4 | 259 | 0.54 | 0.76 | 42 | empty |
| 5 | 129 | 0.52 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1004 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3X1B · Crystal structure of laccase from Lentinus sp. at 1.8 A resolution · 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
- Elsewhere: RCSB PDB 3X1B · PDBe 3X1B
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