MolNFT v1 · #69148 · protein + DNA
DPO4 extension ternary complex with misinserted a opposite the 2- aminofluorene-guanine [AF]G lesion
3KHG · DNA polymerase IV: “DPO4 extension ternary complex with misinserted a opposite the 2- aminofluorene-guanine [AF]G lesion”. X-ray diffraction, 4 ligands (DGT, AF, 2DA), 5 pockets (best druggability 0.79). MolNFT v1 #69148 on…
- PDB
- 3KHG
- Type
- protein + DNA
- Length
- 731 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, AF, 2DA, CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 24% strand | Q97W02 |
| D | 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' | dna | 12 | — | — |
| E | 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP* CP*C)-3' | dna | 19 | — | — |
| H | 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' | dna | 8 | — | — |
| J | 5'-D(*C*CP*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP* CP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, E, B, J
- AF · 2-aminofluorene · ligand · 2 copies · chains A, D, E, H, J
- 2DA · 2',3'-dideoxyadenosine-5'-monophosphate · ligand · chains A, D
- CA · Calcium ion · metal · 6 copies · chains A, D, B, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.79 | 0.80 | 78 | DGT, CA, EPE, AF |
| 2 | 894 | 0.78 | 0.81 | 69 | DGT, CA, AF |
| 3 | 619 | 0.72 | 0.80 | 37 | empty |
| 4 | 524 | 0.68 | 0.79 | 35 | empty |
| 5 | 78 | 0.29 | 0.73 | 15 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1097 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–J · 721 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 565 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–E · 553 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–H · 503 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3KHG · Dpo4 extension ternary complex with misinserted A opposite the 2-aminofluorene-guanine… · the same entry in another collection · chain J against J, 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 0.97
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 3KHG · PDBe 3KHG · UniProt Q97W02
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