Research workbench
Selectivity of nucleoside triphosphate incorporation opposite 1,N2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase DPO4 polymerase
Analyse Selectivity of nucleoside triphosphate incorporation opposite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R8I
- Type
- protein + DNA
- Length
- 371 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'- D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DC)-3')…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DTP, CA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 24% strand | Q97W02 |
| P | DNA (5'- D(*DGP*DGP*DGP*DGP*DGP*DAP*DAP*DGP*DGP*DAP*DTP*DTP*DC)-3') | dna | 13 | — | — |
| T | DNA (5'-D(*DTP*DCP*DAP*DTP*(P) P*DGP*DAP*DAP*DTP*DCP*DCP*DTP*DTP*DCP*DCP*DCP*DCP*DC)-3') | dna | 17 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, 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 | 1135 | 0.79 | 0.81 | 72 | DTP, CA |
| 2 | 616 | 0.72 | 0.80 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1045 Ų buried · 24 hydrogen bonds · protein-nucleic
- P–T · 571 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–P · 571 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2R8I · Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2-Propanodeoxyguanosine… · 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 2R8I · PDBe 2R8I · UniProt Q97W02
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