MolNFT v2 · #159225 · protein + DNA
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with hot-spot sequence" with dGTP"
6NKX · DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3…: “Ternary complex crystal structure of K289M variant of DNA polymerase Beta with hot-spot sequence" with dGTP"”. X-ray diffraction at 1.98, 4 ligands (DGT, NA, MG), 3…
- PDB
- 6NKX
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.98
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- DGT, NA, MG, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.98 · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3') (EC 2.7.7.7) | dna | 16 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') | dna | 10 | — | — |
| D | DNA (5'-D(P*TP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 13% strand | P06746 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains T, P, A
- NA · Sodium ion · metal · 3 copies · chains P, A, D
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 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 | 989 | 0.72 | 0.76 | 69 | MG, DGT |
| 2 | 326 | 0.60 | 0.78 | 30 | empty |
| 3 | 176 | 0.57 | 0.81 | 22 | empty |
Interfaces
5 interfaces between chains.
- T–A · 730 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 448 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- P–A · 390 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 362 Ų buried · 8 hydrogen bonds · protein-nucleic
- T–D · 230 Ų buried · 20 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6NKX · Ternary complex crystal structure of K289M variant of DNA polymerase beta with "hot-spot… · 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 6NKX · PDBe 6NKX · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.