MolNFT v1 · #89406 · protein + DNA
Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate: stereoselective binding of R-isomer
4DOB: “Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta…”. X-ray diffraction, 4 ligands (GRC, NA, MG), 3 pockets (best druggability 0.70). MolNFT v1 #89406 on GenesisL1: 3D structure…
- PDB
- 4DOB
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; C C G a C C G C G C a T C a G C; G C T G a T G C G (doc); G T C G G
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- GRC, 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, 4.2.99.-) | protein | 326 | 51% helix, 13% strand | P06746 |
| T | C C G a C C G C G C a T C a G C | dna | 16 | — | — |
| P | G C T G a T G C G (doc) | dna | 10 | — | — |
| D | G T C G G | dna | 5 | — | — |
Ligands and binding sites
- GRC · 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine · ligand · chains A, T, P
- NA · Sodium ion · metal · 3 copies · chains A, P, D
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 5 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 | 962 | 0.70 | 0.75 | 64 | MG, GRC |
| 2 | 321 | 0.60 | 0.78 | 28 | empty |
| 3 | 229 | 0.56 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–T · 702 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 459 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–D · 368 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–P · 357 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 226 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4DOB · 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 4DOB · PDBe 4DOB · UniProt P06746
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