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
- 1S0O
- Type
- protein + DNA
- Length
- 742 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- TTP, CA, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3' | dna | 13 | — | — |
| D, F | 5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3' | dna | 17 | — | — |
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains D, A, E, F, B
- CA · Calcium ion · metal · 6 copies · chains A, E, B
- MG · Magnesium ion · metal · 2 copies · chains C, A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.80 | 0.82 | 65 | CA, TTP |
| 2 | 629 | 0.78 | 0.84 | 53 | TTP |
| 3 | 343 | 0.75 | 0.86 | 34 | empty |
| 4 | 618 | 0.71 | 0.79 | 41 | empty |
| 5 | 87 | 0.43 | 0.80 | 17 | empty |
Interfaces
9 interfaces between chains.
- F–B · 1048 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–A · 982 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–F · 569 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- E–B · 546 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 540 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 1S0O · Snapshots of replication through an abasic lesion: structural basis for base substitution… · the same entry in another collection · chain B against B, 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 1S0O · PDBe 1S0O · UniProt Q97W02
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