MolNFT v1 · #67503 · protein + DNA
Alternative binding mode of restriction endonuclease bcni to cognate DNA
3IMB · R.BCNI: “Alternative binding mode of restriction endonuclease bcni to cognate DNA”. X-ray diffraction, 14 pockets (best druggability 0.62). MolNFT v1 #67503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IMB
- Type
- protein + DNA
- Length
- 1,024 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R.BCNI; 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3'; 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3'
- UniProt
- Q8RNV8
- Pockets
- 14 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | R.BCNI | protein | 238 | 19% helix, 38% strand | Q8RNV8 |
| E, G, I, K | 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | dna | 9 | — | — |
| F, H, J, L | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3' | dna | 9 | — | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.62 | 0.77 | 42 | empty |
| 2 | 478 | 0.61 | 0.76 | 45 | empty |
| 3 | 506 | 0.61 | 0.75 | 46 | empty |
| 4 | 338 | 0.59 | 0.77 | 36 | empty |
| 5 | 243 | 0.58 | 0.79 | 34 | empty |
Interfaces
25 interfaces between chains.
- B–G · 1077 Ų buried · 30 hydrogen bonds · protein-nucleic
- D–K · 1075 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–E · 1075 Ų buried · 30 hydrogen bonds · protein-nucleic
- C–I · 1071 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–J · 1009 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 3IMB · Alternative binding mode of restriction endonuclease BcnI to cognate DNA · 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 3IMB · PDBe 3IMB · UniProt Q8RNV8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.