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DPO4 extension ternary complex with disordered a opposite an oxog in anti conformation
Analyse DPO4 extension ternary complex with disordered a opposite an oxog in anti… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GII
- 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*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA, NA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 25% strand | Q97W02 |
| D | 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' | dna | 12 | — | — |
| E | 5'-D(*CP*TP*AP*AP*CP*(8OG) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' | dna | 19 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, E
- CA · Calcium ion · metal · 3 copies · chains A, D
- NA · Sodium ion · metal · chains A
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 | 1007 | 0.80 | 0.82 | 63 | DGT, CA |
| 2 | 559 | 0.76 | 0.83 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–E · 1111 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–D · 575 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 561 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3GII · Dpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation · 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 3GII · PDBe 3GII · UniProt Q97W02
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