MolNFT v1 · #128440 · protein
Crystal structure of laccases from pycnoporus sanguineus, izoform II, monoclinic
5NQ9 · Laccase, izoform II: “Crystal structure of laccases from pycnoporus sanguineus, izoform II, monoclinic”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.71). MolNFT v1 #128440 on GenesisL1: 3D…
- PDB
- 5NQ9
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase, izoform II
- EC
- 1.10.3.2
- Ligands
- NAG, MAN, BMA, CU, PER
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Laccase, izoform II (EC 1.10.3.2) | protein | 497 | 11% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- CU · Copper (II) ion · metal · 12 copies · chains A, C
- PER · Peroxide ion · ion · 2 copies · chains A, C
- FMT · Formic acid · additive · 11 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.71 | 0.81 | 53 | empty |
| 2 | 174 | 0.61 | 0.83 | 34 | empty |
| 3 | 144 | 0.54 | 0.81 | 21 | empty |
| 4 | 244 | 0.52 | 0.76 | 32 | empty |
| 5 | 196 | 0.48 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–C · 559 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5NQ9 · Crystal structure of laccases from Pycnoporus sanguineus, izoform II, monoclinic · 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 5NQ9 · PDBe 5NQ9
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