Research workbench
Crystal structure of laccase from myceliophthora thermophila
Analyse Crystal structure of laccase from myceliophthora thermophila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F5K
- Type
- protein
- Length
- 558 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular laccase, LCC1
- UniProt
- G2QG31
- Ligands
- NAG, MAN, BMA, CU, CA, OH
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular laccase, LCC1 | protein | 558 | 13% helix, 39% strand | G2QG31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies
- CU · Copper (II) ion · metal · 4 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- OH · Hydroxide ion · ion · chains A
- 2PE · Nonaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 24 | empty |
| 2 | 52 | 0.60 | 0.92 | 21 | empty |
| 3 | 113 | 0.54 | 0.83 | 25 | NAG |
| 4 | 102 | 0.46 | 0.79 | 24 | empty |
| 5 | 63 | 0.45 | 0.83 | 18 | empty |
Modifications
Observed in the structure: 7 glycan, 3 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 6F5K · Crystal structure of laccase from Myceliophthora thermophila · 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 G2QG31
- Elsewhere: RCSB PDB 6F5K · PDBe 6F5K · UniProt G2QG31
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