MolNFT v1 · #126242 · protein
Crystal structure of a laccase-like multicopper oxidase mcog from aspergillus niger bound to zinc
5LWW: “Crystal structure of a laccase-like multicopper oxidase mcog from aspergillus niger bound to zinc”. X-ray diffraction, 7 ligands (NAG, BMA, MAN), 3 pockets (best druggability 0.57). MolNFT v1 #126242 on GenesisL1: 3D structure…
- PDB
- 5LWW
- Type
- protein
- Length
- 550 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multicopper oxidase
- EC
- 1.10.3.2
- UniProt
- A2QS62
- Ligands
- NAG, BMA, MAN, ZN, CU, K, CL
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multicopper oxidase (EC 1.10.3.2) | protein | 550 | 11% helix, 39% strand | A2QS62 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 8 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.57 | 0.85 | 28 | ZN, CL |
| 2 | 175 | 0.51 | 0.78 | 27 | NAG |
| 3 | 51 | 0.27 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5LWW · Crystal structure of a laccase-like multicopper oxidase McoG from Aspergillus niger bound… · 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 A2QS62
- Elsewhere: RCSB PDB 5LWW · PDBe 5LWW · UniProt A2QS62
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