Research workbench
Pre-catalytic ternary complex of human DNA polymerase beta with gapped DNA substrate incoming (-)3TC-tp and CA2+.
Analyse Pre-catalytic ternary complex of human DNA polymerase beta with gapped DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U2S
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; 5-mer phosphorylated downstream primer; 10- mer primer; 16- mer…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- 1RZ, NA, CA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 48% 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 | 48% helix, 13% strand | P06746 |
| D | 5-mer phosphorylated downstream primer | dna | 5 | — | — |
| P | 10- mer primer | dna | 10 | — | — |
| T | 16- mer template | dna | 16 | — | — |
Ligands and binding sites
- 1RZ · Lamivudine Triphosphate · ligand · chains A, P, T
- NA · Sodium ion · metal · 4 copies · chains A, D, P
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · 6 copies · chains A, P, D, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.74 | 0.77 | 85 | 1RZ, CA, NA, ACT |
| 2 | 226 | 0.61 | 0.82 | 25 | ACT |
| 3 | 58 | 0.32 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–T · 508 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 470 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–D · 384 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–P · 289 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–T · 233 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 5U2S · Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate… · 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 5U2S · PDBe 5U2S · UniProt P06746
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