MolNFT v2 · #193981 · protein + DNA
Binary complex of DNA Polymerase Beta with Ring open Intermediate Fapy-dG in the template position
7S9O: “Binary complex of DNA Polymerase Beta with Ring open Intermediate Fapy-dG in the template position”. X-ray diffraction at 2.23, 1 ligand (NA), 2 pockets (best druggability 0.74). MolNFT v2 #193981 on GenesisL1: 3D structure, binding…
- PDB
- 7S9O
- Type
- protein + DNA
- Length
- 358 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.23
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*C*(IFP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- NA
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.23 · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 327 | 52% helix, 13% strand | P06746 |
| T | DNA (5'-D(*CP*CP*GP*AP*C*(IFP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A*(SO4))-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.74 | 0.77 | 85 | NA |
| 2 | 285 | 0.62 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- T–P · 481 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–T · 472 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 371 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 314 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–D · 237 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7S9O · Binary complex of DNA polymerase beta with ring open intermediate fapy-dg in the template… · the same entry in another collection · chain A against A, TM-score 1.00
- P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P06746
- Elsewhere: RCSB PDB 7S9O · PDBe 7S9O · UniProt P06746
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