MolNFT v2 · #212973 · protein + DNA
DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of azt-tp (1 millimolar) and MNCL2 (5 millimolar)
8ICO · DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'): “DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of…”. X-ray diffraction at 2.7, 3 ligands (AZT, MN, NA), 3 pockets (best druggability…
- PDB
- 8ICO
- Type
- protein + DNA
- Length
- 341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- 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
- AZT, MN, NA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.7 · 3 distinct chains · 51% helix, 12% 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 | 51% helix, 12% strand | P06746 |
Ligands and binding sites
- AZT · 3'-azido-3'-deoxythymidine-5'-triphosphate · ligand · chains P, A
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains P, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.65 | 0.78 | 56 | MN, AZT |
| 2 | 214 | 0.62 | 0.83 | 23 | empty |
| 3 | 52 | 0.24 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- P–A · 325 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 317 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- T–A · 304 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 8ICO · DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with seven base pairs of DNA; soaked… · 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 8ICO · PDBe 8ICO · UniProt P06746
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