MolNFT v1 · #13006 · protein
Active laccase from trametes versicolor complexed with 2,5-xylidine
1KYA: “Active laccase from trametes versicolor complexed with 2,5-xylidine”. X-ray diffraction, 4 ligands (PYE, XYD, NAG), 17 pockets (best druggability 0.72). MolNFT v1 #13006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KYA
- Type
- protein
- Length
- 1,996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- Q96UT7
- Ligands
- PYE, XYD, NAG, CU
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Laccase (EC 1.10.3.2) | protein | 499 | 9% helix, 37% strand | Q96UT7 |
Ligands and binding sites
- PYE · Tetrahydropyran · ligand · 9 copies · chains B, D
- XYD · 2,5-dimethylaniline · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.72 | 0.76 | 84 | XYD |
| 2 | 228 | 0.52 | 0.76 | 42 | empty |
| 3 | 223 | 0.52 | 0.76 | 36 | empty |
| 4 | 127 | 0.49 | 0.79 | 22 | empty |
| 5 | 193 | 0.49 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- C–D · 304 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1KYA · Active laccase from trametes versicolor complexed with 2,5-xylidine · 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 Q96UT7
- Elsewhere: RCSB PDB 1KYA · PDBe 1KYA · UniProt Q96UT7
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