Research workbench
DPO4 extension ternary complex with a C base opposite the 2- aminofluorene-guanine [AF]G lesion
Analyse DPO4 extension ternary complex with a C base opposite the 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KHH
- Type
- protein + DNA
- Length
- 741 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*(DOC))-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, AF, CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 23% strand | Q97W02 |
| D, H | 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3' | dna | 13 | — | — |
| E | 5'-D(*CP*CP*TP*A*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP* CP*C)-3' | dna | 16 | — | — |
| J | 5'-D(*CP*CP*TP*A*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP* CP*C)-3' | dna | 17 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.80 | 0.82 | 88 | DGT, CA |
| 2 | 982 | 0.80 | 0.82 | 80 | DGT, CA |
| 3 | 536 | 0.74 | 0.82 | 39 | AF |
| 4 | 631 | 0.72 | 0.80 | 38 | AF |
| 5 | 299 | 0.62 | 0.79 | 39 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1047 Ų buried · 14 hydrogen bonds · protein-protein
- B–J · 787 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–E · 701 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–E · 602 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- B–H · 591 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 3KHH · Dpo4 extension ternary complex with a C base opposite the 2-aminofluorene-guanine [AF]G… · 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 0.96
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 3KHH · PDBe 3KHH · UniProt Q97W02
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