Research workbench
X-ray structure of E COLI alkb crosslinked to dsdna in the active site
Analyse X-ray structure of E COLI alkb crosslinked to dsdna in the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BKZ
- Type
- protein + DNA
- Length
- 227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb; DNA (5'…
- EC
- 1.14.11.-
- UniProt
- P05050
- Ligands
- AKG, MN
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb (EC 1.14.11.-) | protein | 201 | 15% helix, 34% strand | P05050 |
| B | DNA (5'- D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3') | dna | 13 | — | — |
| C | DNA (5'- D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 207 | 0.59 | 0.82 | 22 | empty |
| 2 | 378 | 0.56 | 0.75 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 623 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 595 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 212 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3BKZ · X-ray structure of E coli AlkB crosslinked to dsDNA in the active site · the same entry in another collection · chain A against A, TM-score 1.00
- P05050 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase alkb… · a predicted model of the same protein · 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 P05050
- Elsewhere: RCSB PDB 3BKZ · PDBe 3BKZ · UniProt P05050
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.