MolNFT v1 · #68234 · protein + DNA
Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monobromo methylene triphosphate
3JPQ: “Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta…”. X-ray diffraction, 4 ligands (GBR, NA, MG), 3 pockets (best druggability 0.70). MolNFT v1 #68234 on GenesisL1: 3D structure…
- PDB
- 3JPQ
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; 5'-D(P*GP*TP*CP*GP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- P06746
- Ligands
- GBR, NA, MG, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7) | protein | 326 | 51% helix, 13% strand | P06746 |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3' | dna | 10 | — | — |
| T | 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
Ligands and binding sites
- GBR · 5'-O-[(R)-{[(S)-[(R)-bromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine · ligand · chains A, P, T
- NA · Sodium ion · metal · 3 copies · chains A, P, D
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.70 | 0.75 | 64 | GBR, MG |
| 2 | 350 | 0.62 | 0.78 | 29 | empty |
| 3 | 216 | 0.58 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–T · 709 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 464 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–D · 370 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–P · 360 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–T · 229 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3JPQ · Ternary complex of DNA polymerase beta with a dideoxy terminated primer and… · 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 0.95
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 3JPQ · PDBe 3JPQ · UniProt P06746
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