Research workbench
Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP
Analyse Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UXP
- Type
- protein + DNA
- Length
- 682 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.723
- Source
- Rattus norvegicus; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase beta; DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'; DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06766
- Ligands
- D3T, NA
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.723 · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 48% helix, 12% strand | P06766 |
| P, D | DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3' | dna | 7 | — | — |
| T, E | DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3' | dna | 8 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · 2 copies · chains A, P, T, B, D, E
- NA · Sodium ion · metal · 7 copies · chains A, P, T, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.63 | 0.75 | 56 | D3T, NA |
| 2 | 310 | 0.62 | 0.79 | 42 | empty |
| 3 | 232 | 0.61 | 0.81 | 30 | empty |
| 4 | 339 | 0.58 | 0.76 | 35 | D3T, NA |
| 5 | 183 | 0.57 | 0.81 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 679 Ų buried · 5 hydrogen bonds · protein-protein
- A–T · 579 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–E · 564 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 363 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 330 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3UXP · Co-crystal structure of rat DNA polymerase beta mutator I260Q: enzyme- DNA-ddttp · the same entry in another collection · chain T against T, TM-score 1.00
- P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P06766
- Elsewhere: RCSB PDB 3UXP · PDBe 3UXP · UniProt P06766
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