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DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of datp (1 millimolar) and MNCL2 (5 millimolar)
Analyse DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with six 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
- 9ICQ
- Type
- protein + DNA
- Length
- 339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3'); DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'); Protein (DNA…
- UniProt
- P06746
- Ligands
- DTP, MN, NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3') | dna | 6 | — | — |
| P | DNA (5'-D(*CP*AP*GP*AP*TP*G)-3') | dna | 6 | — | — |
| A | Protein (DNA polymerase beta (E.C.2.7.7.7)) | protein | 327 | 49% helix, 14% strand | P06746 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains 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
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 | 201 | 0.61 | 0.82 | 23 | empty |
| 2 | 293 | 0.57 | 0.77 | 42 | MN, DTP |
| 3 | 76 | 0.32 | 0.75 | 16 | MN |
| 4 | 50 | 0.23 | 0.72 | 12 | empty |
Interfaces
3 interfaces between chains.
- T–P · 277 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- T–A · 274 Ų buried · 6 hydrogen bonds · protein-nucleic
- P–A · 256 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 9ICQ · DNA polymerase beta (pol B) (E.C.2.7.7.7) complexed with six base pairs of DNA; soaked in… · 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 9ICQ · PDBe 9ICQ · UniProt P06746
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