Research workbench
Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-METHYLADENINE analog
Analyse Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JX7
- Type
- protein + DNA
- Length
- 256 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Bacillus cereus; SYNTHETIC CONSTRUCT
- Molecule
- alkylpurine DNA glycosylase AlkD; DNA (5'-D(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3')…
- UniProt
- Q816E8
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.6 · 3 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | alkylpurine DNA glycosylase AlkD | protein | 232 | 71% helix, 1% strand | Q816E8 |
| B | DNA (5'-D(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3') | dna | 12 | — | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.78 | 0.82 | 46 | empty |
| 2 | 299 | 0.59 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 558 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–C · 527 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 331 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3JX7 · Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing a… · 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 Q816E8
- Elsewhere: RCSB PDB 3JX7 · PDBe 3JX7 · UniProt Q816E8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.