Research workbench
Crystal structure of chimeric mutant of E3L in complex with Z-DNA
Analyse Crystal structure of chimeric mutant of E3L in complex with Z-DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C0I
- Type
- protein + DNA
- Length
- 212 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded RNA-binding PROTEIN,DOUBLE-stranded RNA- specific adenosine deaminase…
- UniProt
- Q86638, P55265
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-binding PROTEIN,DOUBLE-stranded RNA- specific adenosine deaminase | protein | 61 | 54% helix, 11% strand | Q86638, P55265 |
| B | Double-stranded RNA-binding PROTEIN,DOUBLE-stranded RNA- specific adenosine deaminase | protein | 67 | 55% helix, 13% strand | Q86638, P55265 |
| C | Double-stranded RNA-binding PROTEIN,DOUBLE-stranded RNA- specific adenosine deaminase | protein | 65 | 52% helix, 14% strand | Q86638, P55265 |
| D, E | DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3') | dna | 6 | — | — |
| F | DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.43 | 0.75 | 16 | empty |
| 2 | 60 | 0.30 | 0.74 | 12 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1993 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 401 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–E · 382 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 373 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–E · 316 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
- 7C0I · Crystal structure of chimeric mutant of E3L in complex with Z-DNA · the same entry in another collection · chain F against F, TM-score 1.00
- P55265 · AlphaFold monomer V2.0 prediction for double-stranded RNA-specific adenosine deaminase… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q86638
- Every structure of UniProt P55265
- Elsewhere: RCSB PDB 7C0I · PDBe 7C0I · UniProt Q86638 · UniProt P55265
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