MolNFT v1 · #8354 · protein
Crystal structure determination at room temperature of a laccase from trametes versicolor in its oxidised form containing a full complement of copper ions
1GYC · Laccase 2: “Crystal structure determination at room temperature of a laccase from trametes versicolor in its oxidised…”. X-ray diffraction, 2 ligands (NAG, CU), 5 pockets (best druggability 0.54). MolNFT v1 #8354 on GenesisL1: 3D…
- PDB
- 1GYC
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase 2
- EC
- 1.10.3.2
- UniProt
- Q12718
- Ligands
- NAG, CU
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase 2 (EC 1.10.3.2) | protein | 499 | 11% helix, 38% strand | Q12718 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.54 | 0.81 | 21 | empty |
| 2 | 200 | 0.51 | 0.77 | 35 | empty |
| 3 | 115 | 0.45 | 0.78 | 23 | empty |
| 4 | 95 | 0.38 | 0.76 | 17 | empty |
| 5 | 50 | 0.32 | 0.77 | 20 | IPA |
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 1GYC · Crystal structure determination at room temperature of a laccase from trametes versicolor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12718 · AlphaFold monomer V2.0 prediction for laccase-2 (Q12718) · a predicted model of the same protein · 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 Q12718
- Elsewhere: RCSB PDB 1GYC · PDBe 1GYC · UniProt Q12718
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