MolNFT v1 · #54020 · protein + DNA
Binary complex of sulfolobus solfataricus DPO4 DNA polymerase and 1,N2-ethenoguanine modified DNA, magnesium form
2XC9 · DNA polymerase IV: “Binary complex of sulfolobus solfataricus DPO4 DNA polymerase and 1,N2-ethenoguanine modified DNA, magnesium…”. X-ray diffraction, 2 pockets (best druggability 0.80). MolNFT v1 #54020 on GenesisL1: 3D structure…
- PDB
- 2XC9
- Type
- protein + DNA
- Length
- 371 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 46% helix, 25% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3' | dna | 14 | — | — |
| T | 5'-D(*TP*CP*AP*CP*GNEP*GP*AP*AP*TP*CP*CP*TP*TP* CP*CP*CP*CP*C)-3' | dna | 16 | — | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.80 | 0.82 | 78 | empty |
| 2 | 344 | 0.70 | 0.83 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–T · 886 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 683 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 673 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2XC9 · Binary complex of sulfolobus solfataricus DPO4 DNA polymerase and 1, N2-ethenoguanine… · the same entry in another collection · chain A against A, 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 2XC9 · PDBe 2XC9 · UniProt Q97W02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.