Research workbench
Fidelity of DPO4: effect of metal ions, nucleotide selection and pyrophosphorolysis
Analyse Fidelity of DPO4: effect of metal ions, nucleotide selection and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AGO
- Type
- protein + DNA
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- POP, MG, CA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'- D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*G)-3') | dna | 14 | — | — |
| C | DNA (5'- D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 17 | — | — |
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 23% strand | Q97W02 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains B, A
- MG · Magnesium ion · metal · 4 copies · chains B, A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.79 | 0.81 | 70 | CA, POP |
| 2 | 427 | 0.71 | 0.82 | 38 | empty |
| 3 | 63 | 0.39 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–A · 948 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–A · 622 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 615 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 2AGO · Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis · the same entry in another collection · chain B against B, 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 2AGO · PDBe 2AGO · UniProt Q97W02
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