MolNFT v1 · #86543 · protein + DNA
Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dg DNA lesion -da basepair in the post-insertion site.
4B9U: “Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dg DNA lesion -da…”. X-ray diffraction, 2 ligands (MG, SO4), 10 pockets (best druggability 0.70). MolNFT v1 #86543 on GenesisL1: 3D structure…
- PDB
- 4B9U
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3'…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | E1C9K5 |
| B | 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*AP)-3' | dna | 11 | — | — |
| C | 5'-D(*CP*AP*AP*FOXP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.70 | 0.95 | 25 | empty |
| 2 | 973 | 0.70 | 0.75 | 65 | SO4, MG |
| 3 | 306 | 0.70 | 0.84 | 32 | empty |
| 4 | 368 | 0.67 | 0.81 | 44 | SO4 |
| 5 | 272 | 0.63 | 0.80 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 977 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 913 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 497 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B9U · 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 4B9U · PDBe 4B9U · UniProt E1C9K5
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