MolNFT v1 · #191495 · 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 datp (1 millimolar), MGCL2 (5 millimolar), and MNCL2 (5 millimolar)
8ICK · 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, 3 ligands (DTP, MN, NA), 5 pockets (best druggability 0.65).…
- PDB
- 8ICK
- Type
- protein + DNA
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'); DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*A)-3'); Protein…
- UniProt
- P06746
- Ligands
- DTP, MN, NA
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 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*GP*A)-3') | dna | 8 | — | — |
| A | Protein (DNA polymerase beta (E.C.2.7.7.7)) | protein | 327 | 50% helix, 14% strand | P06746 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains P, A
- MN · Manganese (II) ion · metal · 2 copies · chains P, A
- 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.65 | 0.83 | 27 | empty |
| 2 | 202 | 0.61 | 0.83 | 22 | empty |
| 3 | 133 | 0.41 | 0.75 | 23 | empty |
| 4 | 88 | 0.38 | 0.77 | 22 | MN, DTP |
| 5 | 87 | 0.30 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- P–A · 453 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 319 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- T–A · 297 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 8ICK · 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 T against T, 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 8ICK · PDBe 8ICK · UniProt P06746
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