Research workbench
The structure of C160S,C508S,C578S mutant of NT.BSPD6I nicking endonuclease at 0.185 nm resolution .
Analyse The structure of C160S,C508S,C578S mutant of NT.BSPD6I nicking endonuclease at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LIQ
- Type
- protein
- Length
- 1,166 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicking endonuclease N.BSPD6I
- UniProt
- Q8GCA3
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicking endonuclease N.BSPD6I | protein | 583 | 62% helix, 10% strand | Q8GCA3 |
| B | Nicking endonuclease N.BSPD6I | protein | 583 | 62% helix, 9% strand | Q8GCA3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.76 | 0.80 | 92 | GOL, PO4 |
| 2 | 899 | 0.75 | 0.79 | 98 | GOL, PO4 |
| 3 | 332 | 0.55 | 0.75 | 31 | GOL |
| 4 | 276 | 0.53 | 0.75 | 35 | empty |
| 5 | 173 | 0.49 | 0.77 | 24 | GOL |
Interfaces
1 interface between chains.
- A–B · 51 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5LIQ · The structure of C160S,C508S,C578S mutant of Nt.BspD6I nicking endonuclease at 0.185 nm… · 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 Q8GCA3
- Elsewhere: RCSB PDB 5LIQ · PDBe 5LIQ · UniProt Q8GCA3
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