Research workbench
Ternary complex crystal structure of K289M variant of DNA polymerase beta with dgtp
Analyse Ternary complex crystal structure of K289M variant of DNA polymerase beta with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NKR
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(P*GP*TP*CP*GP*G)-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 · 4 distinct chains · 51% helix, 14% 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, 14% strand | P06746 |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| P | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3') | dna | 10 | — | — |
| T | DNA (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
- DGT · 2'-deoxyguanosine-5'-triphosphate · 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 · 2 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 | 970 | 0.72 | 0.76 | 64 | MG, DGT |
| 2 | 374 | 0.60 | 0.77 | 32 | empty |
| 3 | 210 | 0.57 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–T · 695 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 468 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–D · 403 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 349 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–T · 231 Ų buried · 22 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6NKR · Ternary complex crystal structure of K289M variant of DNA polymerase Beta with dGTP · 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 0.94
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 6NKR · PDBe 6NKR · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.