MolNFT v1 · #122819 · protein + DNA
Binary complex crystal structure of DNA polymerase beta with T:G mismatch at the primer terminus
5J0X: “Binary complex crystal structure of DNA polymerase beta with T:G mismatch at the primer terminus”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.69). MolNFT v1 #122819 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5J0X
- Type
- protein + DNA
- Length
- 359 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
- NA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 328 | 50% helix, 13% strand | P06746 |
| T | Template strand | dna | 16 | — | — |
| P | Primer strand | dna | 10 | — | — |
| D | Downstream primer strand | dna | 5 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, P, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.69 | 0.76 | 73 | NA |
| 2 | 247 | 0.64 | 0.83 | 26 | empty |
| 3 | 86 | 0.34 | 0.75 | 12 | empty |
| 4 | 65 | 0.33 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- T–P · 487 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–T · 402 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 387 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–P · 342 Ų buried · 7 hydrogen bonds · protein-nucleic
- T–D · 229 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 5J0X · Binary complex crystal structure of DNA polymerase Beta with T:G 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 0.93
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 5J0X · PDBe 5J0X · UniProt P06746
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