MolNFT v1 · #122870 · protein + DNA
Ternary complex crystal structure of DNA polymerase beta with G:A mismatch at the primer terminus
5J2F: “Ternary complex crystal structure of DNA polymerase beta with G:A mismatch at the primer terminus”. X-ray diffraction, 4 ligands (DUP, MG, NA), 3 pockets (best druggability 0.71). MolNFT v1 #122870 on GenesisL1: 3D structure…
- PDB
- 5J2F
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; Template strand; Primer strand; Downstream primer strand
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- DUP, MG, NA, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 50% 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 | 50% helix, 14% strand | P06746 |
| T | Template strand | dna | 16 | — | — |
| P | Primer strand | dna | 10 | — | — |
| D | Downstream primer strand | dna | 5 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, D
- CL · Chloride ion · ion · 5 copies · chains A, P
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 | 940 | 0.71 | 0.76 | 63 | DUP, MG |
| 2 | 329 | 0.61 | 0.78 | 28 | empty |
| 3 | 228 | 0.58 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–T · 738 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 460 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–P · 371 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 370 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 231 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Compared structures
- 5J2F · Ternary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer… · 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 5J2F · PDBe 5J2F · UniProt P06746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.