Research workbench
Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dg DNA lesion outside of the pre-insertion site.
Analyse Structure of the high fidelity DNA polymerase I with an oxidative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B9S
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(*AP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 579 | 56% helix, 14% strand | E1C9K5 |
| B | 5'-D(*AP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3' | dna | 10 | — | — |
| C | 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*TP*TP)-3' | dna | 12 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.70 | 0.84 | 34 | empty |
| 2 | 400 | 0.69 | 0.81 | 44 | GLC, FRU, SO4 |
| 3 | 51 | 0.69 | 0.98 | 20 | empty |
| 4 | 240 | 0.62 | 0.81 | 30 | empty |
| 5 | 563 | 0.61 | 0.74 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1035 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 835 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 441 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B9S · Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG… · the same entry in another collection · chain A against A, TM-score 1.00
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 E1C9K5
- Elsewhere: RCSB PDB 4B9S · PDBe 4B9S · UniProt E1C9K5
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