Research workbench
Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-da DNA lesion -thymine basepair in the post-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
- 4B9M
- Type
- protein + DNA
- Length
- 603 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*TP)-3'…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | E1C9K5 |
| B | 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*TP*TP)-3' | dna | 11 | — | — |
| C | 5'-D(*DC*DA*DA*FAX*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3' | dna | 12 | — | — |
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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.76 | 0.94 | 23 | empty |
| 2 | 953 | 0.71 | 0.76 | 72 | MG, SO4 |
| 3 | 145 | 0.69 | 0.90 | 21 | empty |
| 4 | 360 | 0.68 | 0.81 | 43 | SO4 |
| 5 | 260 | 0.61 | 0.79 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 839 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 816 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 498 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B9M · Structure of the high fidelity DNA polymerase I with an 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 4B9M · PDBe 4B9M · UniProt E1C9K5
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