Research workbench
Crystal structure of the site-specific DNA nickase N.BSPD6I
Analyse Crystal structure of the site-specific DNA nickase N.BSPD6I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EWF
- Type
- protein
- Length
- 587 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicking endonuclease N.BSPD6I
- UniProt
- Q8GCA3
- Ligands
- BR
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicking endonuclease N.BSPD6I | protein | 587 | 61% helix, 9% strand | Q8GCA3 |
Ligands and binding sites
- BR · Bromide ion · ion · 13 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.74 | 0.80 | 73 | BR |
| 2 | 214 | 0.49 | 0.75 | 26 | BR |
| 3 | 142 | 0.42 | 0.75 | 23 | empty |
| 4 | 84 | 0.38 | 0.77 | 21 | empty |
| 5 | 61 | 0.36 | 0.78 | 14 | empty |
Compared structures
- 2EWF · Crystal structure of the site-specific DNA nickase N.BspD6I · 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 2EWF · PDBe 2EWF · UniProt Q8GCA3
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