Research workbench
Crystal structure of laccases from pycnoporus sanguineus, izoform II
Analyse Crystal structure of laccases from pycnoporus sanguineus, izoform II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQ8
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- UniProt
- Q96TR6
- Ligands
- ME2, IPH, NAG, MAN, BMA, CU, NA, PER
- Pockets
- 4 · 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 | protein | 497 | 11% helix, 38% strand | Q96TR6 |
Ligands and binding sites
- ME2 · 1-ethoxy-2-(2-methoxyethoxy)ethane · ligand · 2 copies · chains A
- IPH · Phenol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- BMA · beta-D-mannopyranose · sugar
- CU · Copper (II) ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- PER · Peroxide ion · ion · chains A
- MLI · Malonate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.50 | 0.80 | 17 | empty |
| 2 | 196 | 0.47 | 0.75 | 31 | NA |
| 3 | 90 | 0.43 | 0.79 | 19 | empty |
| 4 | 120 | 0.37 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5NQ8 · Crystal structure of laccases from Pycnoporus sanguineus, izoform II · 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 Q96TR6
- Elsewhere: RCSB PDB 5NQ8 · PDBe 5NQ8 · UniProt Q96TR6
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