Research workbench
Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-da DNA lesion in the pre-insertion site.
Analyse Structure of the high fidelity DNA polymerase I with the oxidative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B9L
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3'…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- GLC, FRU, MG, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | E1C9K5 |
| B | 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP)-3' | dna | 10 | — | — |
| C | 5'-D(*CP*AP*GP*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' | dna | 11 | — | — |
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 · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.69 | 0.81 | 46 | GLC, FRU |
| 2 | 273 | 0.69 | 0.85 | 37 | empty |
| 3 | 738 | 0.68 | 0.76 | 63 | MG, SO4 |
| 4 | 115 | 0.45 | 0.78 | 23 | empty |
| 5 | 73 | 0.43 | 0.80 | 13 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 1183 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 789 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 455 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B9L · Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA… · 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 4B9L · PDBe 4B9L · UniProt E1C9K5
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