MolNFT v2 · #48697 · protein + DNA
RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX
2Q10 · DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'): “RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX”. X-ray diffraction at 1.75, 2 ligands (CA, CL), 11 pockets (best druggability 0.67). MolNFT v2 #48697 on…
- PDB
- 2Q10
- Type
- protein + DNA
- Length
- 520 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Brevibacillus centrosporus; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'); DNA…
- UniProt
- Q8RNV8
- Ligands
- CA, CL
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.75 · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3') | dna | 11 | — | — |
| D, F | DNA (5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3') | dna | 11 | — | — |
| A, B | R.BcnI | protein | 238 | 19% helix, 40% strand | Q8RNV8 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains C, A, E, B
- CL · Chloride ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.67 | 0.80 | 61 | CL |
| 2 | 227 | 0.51 | 0.76 | 24 | empty |
| 3 | 161 | 0.48 | 0.77 | 25 | empty |
| 4 | 136 | 0.46 | 0.78 | 17 | empty |
| 5 | 110 | 0.39 | 0.76 | 19 | empty |
Interfaces
11 interfaces between chains.
- E–B · 990 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–A · 965 Ų buried · 27 hydrogen bonds · protein-nucleic
- D–A · 946 Ų buried · 22 hydrogen bonds · protein-nucleic
- F–B · 915 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 561 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 2Q10 · Restriction endonuclease bcni (wild type)-cognate DNA substrate complex · 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 Q8RNV8
- Elsewhere: RCSB PDB 2Q10 · PDBe 2Q10 · UniProt Q8RNV8
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