MolNFT v1 · #81939 · protein + DNA
Co-crystal structure of K72E variant of rat polymerase beta: enzyme- DNA binary complex
3V7K · DNA polymerase beta: “Co-crystal structure of K72E variant of rat polymerase beta: enzyme- DNA binary complex”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability 0.69). MolNFT v1 #81939 on GenesisL1: 3D structure…
- PDB
- 3V7K
- Type
- protein + DNA
- Length
- 349 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta; DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06766
- Ligands
- NA
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 331 | 50% helix, 12% strand | P06766 |
| P | DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3') | dna | 8 | — | — |
| T | DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.69 | 0.77 | 78 | NA |
| 2 | 207 | 0.60 | 0.82 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–T · 496 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 334 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–P · 312 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3V7K · Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex · the same entry in another collection · chain A against A, TM-score 1.00
- P06766 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06766) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P06766
- Elsewhere: RCSB PDB 3V7K · PDBe 3V7K · UniProt P06766
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