MolNFT v1 · #161744 · protein
Crystal structure of the site-specific DNA nickase N.BSPD6I E418A mutant
6QNZ · Heterodimeric restriction endonuclease R.BSPD6I large…: “Crystal structure of the site-specific DNA nickase N.BSPD6I E418A mutant”. X-ray diffraction, 1 ligand (PO4), 17 pockets (best druggability 0.76). MolNFT v1 #161744 on…
- PDB
- 6QNZ
- Type
- protein
- Length
- 1,142 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heterodimeric restriction endonuclease R.BSPD6I large subunit
- UniProt
- A3FEV7
- Ligands
- PO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heterodimeric restriction endonuclease R.BSPD6I large subunit | protein | 575 | 62% helix, 10% strand | A3FEV7 |
| B | Heterodimeric restriction endonuclease R.BSPD6I large subunit | protein | 567 | 62% helix, 9% strand | A3FEV7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.76 | 0.81 | 71 | PO4 |
| 2 | 718 | 0.75 | 0.81 | 77 | GOL, PO4 |
| 3 | 338 | 0.55 | 0.75 | 33 | empty |
| 4 | 284 | 0.52 | 0.74 | 31 | empty |
| 5 | 76 | 0.51 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 296 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6QNZ · Crystal structure of the site-specific DNA nickase N.BspD6I E418A Mutant · 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 A3FEV7
- Elsewhere: RCSB PDB 6QNZ · PDBe 6QNZ · UniProt A3FEV7
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