MolNFT v2 · #155787 · protein
Crystal Structure of the Zea Mays laccase 3 complexed with coniferyl
6KLJ: “Crystal Structure of the Zea Mays laccase 3 complexed with coniferyl”. X-ray diffraction at 1.998, 4 ligands (CIY, NAG, CU), 6 pockets (best druggability 0.61). MolNFT v2 #155787 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6KLJ
- Type
- protein
- Length
- 547 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.998
- Source
- Zea mays
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- Q2PAJ1
- Ligands
- CIY, NAG, CU, OXY
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.998 · 1 distinct chain · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase (EC 1.10.3.2) | protein | 547 | 11% helix, 40% strand | Q2PAJ1 |
Ligands and binding sites
- CIY · (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- OXY · Oxygen molecule · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.61 | 0.82 | 34 | GOL |
| 2 | 203 | 0.52 | 0.77 | 32 | empty |
| 3 | 51 | 0.50 | 0.87 | 16 | empty |
| 4 | 75 | 0.46 | 0.82 | 17 | CIY |
| 5 | 53 | 0.45 | 0.84 | 15 | NAG |
Modifications
Observed in the structure: 7 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6KLJ · Crystal structure of the zea mays laccase 3 complexed with coniferyl · 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 Q2PAJ1
- Elsewhere: RCSB PDB 6KLJ · PDBe 6KLJ · UniProt Q2PAJ1
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