MolNFT v1 · #52723 · protein + DNA
Ternary complex of DPO4 bound to N2,N2-dimethyl- deoxyguanosine modified DNA with incoming dgtp
2W9A · DNA polymerase IV: “Ternary complex of DPO4 bound to N2,N2-dimethyl- deoxyguanosine modified DNA with incoming dgtp”. X-ray diffraction, 2 ligands (DGT, MG), 3 pockets (best druggability 0.75). MolNFT v1 #52723 on GenesisL1: 3D…
- PDB
- 2W9A
- Type
- protein + DNA
- Length
- 372 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*DOC)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, MG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 46% helix, 24% strand | Q97W02 |
| P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3' | dna | 14 | — | — |
| T | 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*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, P, T
- MG · Magnesium ion · metal · 4 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.75 | 0.80 | 55 | DGT, MG |
| 2 | 593 | 0.74 | 0.82 | 37 | empty |
| 3 | 453 | 0.74 | 0.84 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–T · 842 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 644 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–T · 597 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2W9A · Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming… · the same entry in another collection · chain P against P, 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 2W9A · PDBe 2W9A · UniProt Q97W02
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