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The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus solfataricus DNA Polymerase IV: Steady-state and Pre-steady-state Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing
Analyse The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JEG
- Type
- protein + DNA
- Length
- 373 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.38
- Source
- SULFOLOBUS SOLFATARICUS; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.38 · 3 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 44% helix, 25% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3' | dna | 14 | — | — |
| T | 5'-D(*TP*CP*AP*C BZGP*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, T
- CA · Calcium ion · metal · 4 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.76 | 0.82 | 44 | empty |
| 2 | 653 | 0.73 | 0.80 | 46 | DGT, CA |
| 3 | 446 | 0.73 | 0.83 | 37 | empty |
| 4 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–T · 988 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 636 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 593 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2JEG · The molecular basis of selectivity of nucleoside triphosphate incorporation opposite… · 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 2JEG · PDBe 2JEG · UniProt Q97W02
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