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Single crystal serial study of the inhibition of laccases from steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. fourteenth structure of the series with 5600 kgy dose (data was collected after refreezing).
Analyse Single crystal serial study of the inhibition of laccases from steccherinum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RIL
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase 2
- EC
- 1.10.3.2
- UniProt
- I1VE66
- Ligands
- NAG, CU, OXY, F
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase 2 (EC 1.10.3.2) | protein | 497 | 12% helix, 37% strand | I1VE66 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- OXY · Oxygen molecule · ion · 2 copies · chains A
- F · Fluoride ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.50 | 0.82 | 17 | empty |
| 2 | 169 | 0.46 | 0.75 | 31 | empty |
| 3 | 111 | 0.44 | 0.78 | 23 | empty |
| 4 | 160 | 0.43 | 0.74 | 32 | empty |
| 5 | 90 | 0.36 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6RIL · Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi… · 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 I1VE66
- Elsewhere: RCSB PDB 6RIL · PDBe 6RIL · UniProt I1VE66
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