Research workbench
The structure of D456A mutant of NT.BSPD6I nicking endonuclease at 0.24 nm resolution .
Analyse The structure of D456A mutant of NT.BSPD6I nicking endonuclease at 0.24 nm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LHC
- Type
- protein
- Length
- 1,161 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
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicking endonuclease N.BSPD6I | protein | 579 | 62% helix, 9% strand | Q8GCA3 |
| B | Nicking endonuclease N.BSPD6I | protein | 582 | 60% helix, 9% strand | Q8GCA3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.77 | 0.81 | 83 | GOL, PO4 |
| 2 | 680 | 0.75 | 0.81 | 73 | PO4 |
| 3 | 318 | 0.53 | 0.74 | 35 | GOL |
| 4 | 283 | 0.51 | 0.74 | 31 | empty |
| 5 | 149 | 0.51 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 118 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LHC · The structure of D456A mutant of Nt.BspD6I nicking endonuclease at 0.24 nm resolution . · 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 5LHC · PDBe 5LHC · UniProt Q8GCA3
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