Research workbench
Complex structure of sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4- difluorotoluene nucleotide in the template strand
Analyse Complex structure of sulfolobus solfataricus DPO4 and DNA duplex containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V9W
- Type
- protein + DNA
- Length
- 745 residues
- Chains
- 6
- 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*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DCT, CA
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 343 | 42% helix, 19% strand | Q97W02 |
| B | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 43% helix, 23% strand | Q97W02 |
| C, E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*G)-3' | dna | 13 | — | — |
| D | 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 18 | — | — |
| F | 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · chains A, C, D, B, E, F
- CA · Calcium ion · metal · 4 copies · chains A, C, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.83 | 0.84 | 104 | CA, DCT |
| 2 | 1154 | 0.79 | 0.81 | 78 | CA, DCT |
| 3 | 748 | 0.77 | 0.82 | 55 | empty |
| 4 | 600 | 0.74 | 0.82 | 40 | empty |
| 5 | 108 | 0.54 | 0.83 | 18 | empty |
Interfaces
8 interfaces between chains.
- B–F · 1086 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–D · 1085 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 617 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 605 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–E · 600 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2V9W · Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic… · the same entry in another collection · chain F against F, 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 2V9W · PDBe 2V9W · UniProt Q97W02
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