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
- 2AGP
- Type
- protein + DNA
- Length
- 742 residues
- Chains
- 6
- 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*(DOC)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, MG, CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC)-3') | dna | 13 | — | — |
| D, F | DNA (5'- D(*TP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 17 | — | — |
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 26% strand | Q97W02 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains C, D, A, E, F, B
- MG · Magnesium ion · metal · 5 copies · chains C, A, B, E
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.80 | 0.82 | 74 | CA, MG, DGT |
| 2 | 952 | 0.75 | 0.78 | 63 | CA, DGT |
| 3 | 648 | 0.74 | 0.81 | 38 | empty |
| 4 | 450 | 0.71 | 0.81 | 42 | empty |
| 5 | 82 | 0.45 | 0.81 | 17 | empty |
Interfaces
9 interfaces between chains.
- D–A · 1025 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–B · 975 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 581 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- C–D · 568 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- C–A · 557 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2AGP · 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 B 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 2AGP · PDBe 2AGP · UniProt Q97W02
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