MolNFT v1 · #51526 · protein + DNA
Complex structure of sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4- difluorotoluene nucleotide in the template strand
2VA3 · DNA polymerase IV: “Complex structure of sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere…”. X-ray diffraction, 2 ligands (DGT, CA), 2 pockets (best druggability 0.78). MolNFT v1 #51526 on…
- PDB
- 2VA3
- 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 *CP*TP*A)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 40% helix, 22% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3' | dna | 13 | — | — |
| T | 5'-D(*TP*TP*CP*AP*DFTP*TP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, T
- CA · Calcium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 956 | 0.78 | 0.81 | 64 | DGT, CA |
| 2 | 482 | 0.70 | 0.81 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–T · 933 Ų buried · 26 hydrogen bonds · protein-nucleic
- P–T · 565 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–P · 544 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2VA3 · Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic… · 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 2VA3 · PDBe 2VA3 · UniProt Q97W02
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