Research workbench
DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with seven base pairs of DNA
Analyse DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with seven base pairs of DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 9ICJ
- Type
- protein + DNA
- Length
- 341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'); DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'); Protein (DNA…
- UniProt
- P06746
- Ligands
- NA, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · resolution 3.1 · 3 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3') | dna | 7 | — | — |
| P | DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3') | dna | 7 | — | — |
| A | Protein (DNA polymerase beta (E.C.2.7.7.7)) | protein | 327 | 50% helix, 14% strand | P06746 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.65 | 0.80 | 43 | empty |
| 2 | 211 | 0.61 | 0.82 | 22 | empty |
| 3 | 102 | 0.36 | 0.75 | 14 | empty |
| 4 | 65 | 0.27 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- P–A · 354 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 323 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- T–A · 297 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 9ICJ · DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with seven base pairs of DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P06746
- Elsewhere: RCSB PDB 9ICJ · PDBe 9ICJ · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.