MolNFT v1 · #107463 · protein + DNA
DNA polymerase beta closed product complex with a templating cytosine and 8-oxodgmp, 60 S
4UB3 · 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3': “DNA polymerase beta closed product complex with a templating cytosine and 8-oxodgmp, 60 S”. X-ray diffraction, 3 ligands (PPV, MG, NA), 3 pockets (best druggability 0.69).…
- PDB
- 4UB3
- Type
- protein + DNA
- Length
- 355 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- PPV, MG, NA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3' | dna | 11 | — | — |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 323 | 52% helix, 13% strand | P06746 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains P, A
- MG · Magnesium ion · metal · 2 copies · chains P, A
- NA · Sodium ion · metal · chains P, 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 | 880 | 0.69 | 0.75 | 61 | MG, PPV |
| 2 | 341 | 0.62 | 0.79 | 29 | empty |
| 3 | 213 | 0.56 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- T–A · 709 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–A · 563 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 516 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- D–A · 369 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 239 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4UB3 · DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s · the same entry in another collection · chain T against T, 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 4UB3 · PDBe 4UB3 · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.