Research workbench
Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs
Analyse Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UVU
- Type
- protein + DNA
- Length
- 374 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- SULFOLOBUS SOLFATARICUS; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.7 · 3 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 343 | 45% helix, 23% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3' | dna | 14 | — | — |
| T | 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3' | dna | 17 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.81 | 0.83 | 75 | DGT, CA |
| 2 | 664 | 0.74 | 0.81 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–T · 899 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–T · 618 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–P · 604 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2UVU · Crystal structures of mutant DPO4 DNA polymerases with 8- oxog containing DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q97W02
- Elsewhere: RCSB PDB 2UVU · PDBe 2UVU · UniProt Q97W02
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