Research workbench
DPO4 extension ternary complex with OXOG(SYN)-A(ANTI) and OXOG(ANTI)- A(SYN) pairs
Analyse DPO4 extension ternary complex with OXOG(SYN)-A(ANTI) and OXOG(ANTI)- A(SYN)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GIJ
- Type
- protein + DNA
- Length
- 740 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, CA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 25% strand | Q97W02 |
| D, H | 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' | dna | 13 | — | — |
| E | 5'-D(*CP*TP*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3' | dna | 18 | — | — |
| J | 5'-D(*CP*TP*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3' | dna | 14 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, D, E, B, H, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.79 | 0.81 | 91 | DGT, CA |
| 2 | 1099 | 0.79 | 0.81 | 82 | DGT, CA |
| 3 | 520 | 0.73 | 0.81 | 42 | empty |
| 4 | 544 | 0.72 | 0.81 | 41 | empty |
| 5 | 73 | 0.39 | 0.79 | 15 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1128 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–J · 777 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–H · 674 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–D · 664 Ų buried · 20 hydrogen bonds · protein-nucleic
- H–J · 600 Ų buried · 74 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3GIJ · Dpo4 extension ternary complex with oxoG(syn)-A(anti) and oxoG(anti)-A(syn) pairs · 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 3GIJ · PDBe 3GIJ · UniProt Q97W02
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