Research workbench
Dpo4 post-extension ternary complex with misinserted A opposite the 2-aminofluorene-guanine [AF]G lesion
Analyse Dpo4 post-extension ternary complex with misinserted A opposite the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KHL
- Type
- protein + DNA
- Length
- 743 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Sulfolobus solfataricus P2; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; 5'-D(*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*AP*(DDG))-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- TTP, AF, CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
| D, H | 5'-D(*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*AP*(DDG))-3' | dna | 13 | — | — |
| E | 5'-D(*CP*C*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' | dna | 17 | — | — |
| J | 5'-D(*CP*C*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' | dna | 18 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, D, E, B, H, J
- AF · 2-aminofluorene · ligand · 2 copies · chains A, E, B, J
- CA · Calcium ion · metal · 6 copies · chains A, D, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.80 | 0.82 | 83 | TTP, CA |
| 2 | 1145 | 0.80 | 0.82 | 77 | TTP, CA |
| 3 | 569 | 0.73 | 0.81 | 44 | AF |
| 4 | 535 | 0.72 | 0.81 | 42 | AF |
| 5 | 186 | 0.54 | 0.79 | 34 | empty |
Interfaces
7 interfaces between chains.
- B–J · 1055 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 999 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 691 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–E · 653 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- H–J · 622 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
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 3KHL · PDBe 3KHL · UniProt Q97W02
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