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Ternary complex crystal structure of DNA polymerase beta with T:C mismatch at the primer terminus
Analyse Ternary complex crystal structure of DNA polymerase beta with T:C mismatch at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J2I
- 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
- Pockets
- 3 · best druggability 0.78
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 | 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
- NA · Sodium ion · metal · 2 copies · chains A, P, D
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 | 1029 | 0.78 | 0.80 | 70 | DUP, MG |
| 2 | 322 | 0.63 | 0.80 | 30 | empty |
| 3 | 237 | 0.58 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–T · 727 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 442 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–P · 402 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 399 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 236 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 5J2I · Ternary complex crystal structure of DNA polymerase Beta with T:C 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 0.94
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 5J2I · PDBe 5J2I · UniProt P06746
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