MolNFT v1 · #61344 · protein
Crystal structure of laccase from cerrena maxima at 1.76A resolution
3DIV: “Crystal structure of laccase from cerrena maxima at 1.76A resolution”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 4 pockets (best druggability 0.53). MolNFT v1 #61344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DIV
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- Ligands
- NAG, MAN, BMA, CU
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase (EC 1.10.3.2) | protein | 499 | 11% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CU · Copper (II) ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.53 | 0.82 | 21 | empty |
| 2 | 202 | 0.51 | 0.77 | 32 | empty |
| 3 | 91 | 0.43 | 0.79 | 18 | empty |
| 4 | 118 | 0.39 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 3DIV · Crystal structure of laccase from Cerrena maxima at 1.76A 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 3DIV · PDBe 3DIV
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