MolNFT v2 · #212975 · 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 of datp (0.1 millimolar) and MNCL2 (0.5 millimolar)
8ICQ · 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 3, 1 ligand (NA), 4 pockets (best druggability 0.64).…
- PDB
- 8ICQ
- Type
- protein + DNA
- Length
- 341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- 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
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 3 · 3 distinct chains · 49% helix, 13% 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 | 49% helix, 13% strand | P06746 |
Ligands and binding sites
- 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
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 | 327 | 0.64 | 0.80 | 40 | empty |
| 2 | 217 | 0.62 | 0.83 | 23 | empty |
| 3 | 87 | 0.36 | 0.76 | 19 | empty |
| 4 | 50 | 0.24 | 0.73 | 10 | empty |
Interfaces
3 interfaces between chains.
- P–A · 350 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–P · 319 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- T–A · 299 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 8ICQ · 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 0.79
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 8ICQ · PDBe 8ICQ · UniProt P06746
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