Research workbench
Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift
Analyse Snapshots of replication through an abasic lesion: structural basis for base… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S0N
- Type
- protein + DNA
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Sulfolobus solfataricus; SYNTHETIC CONSTRUCT
- Molecule
- 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*AP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DCP, CA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*AP*CP*G)-3' | dna | 13 | — | — |
| T | 5'-D(*TP*AP*CP*GP*AP*CP*GP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3' | dna | 18 | — | — |
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 25% strand | Q97W02 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, T, A
- CA · Calcium ion · metal · 3 copies · chains P, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.80 | 0.82 | 75 | CA, DCP |
| 2 | 642 | 0.77 | 0.83 | 43 | empty |
| 3 | 60 | 0.42 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1005 Ų buried · 23 hydrogen bonds · protein-nucleic
- P–T · 619 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- P–A · 569 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 1S0N · Snapshots of replication through an abasic lesion: structural basis for base substitution… · 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 1S0N · PDBe 1S0N · UniProt Q97W02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.