Research workbench
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
- 2JEJ
- Type
- protein + DNA
- Length
- 374 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*CP*G)-3' | dna | 15 | — | — |
| T | 5'-D(*TP*CP*AP*C BZGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 18 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, P, 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
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 | 1055 | 0.80 | 0.82 | 86 | CA, DGT |
| 2 | 569 | 0.77 | 0.84 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–T · 996 Ų buried · 26 hydrogen bonds · protein-nucleic
- P–T · 691 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–P · 682 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2JEJ · 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 2JEJ · PDBe 2JEJ · UniProt Q97W02
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