MolNFT v1 · #81940 · protein
Apo structure of rat DNA polymerase beta K72E variant
3V7L: “Apo structure of rat DNA polymerase beta K72E variant”. X-ray diffraction, 3 ligands (NA, CL, SO4), 4 pockets (best druggability 0.63). MolNFT v1 #81940 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3V7L
- Type
- protein
- Length
- 325 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06766
- Ligands
- NA, CL, SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 37% helix, 12% strand | P06766 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
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 | 351 | 0.63 | 0.79 | 30 | empty |
| 2 | 82 | 0.52 | 0.84 | 15 | empty |
| 3 | 55 | 0.33 | 0.77 | 14 | empty |
| 4 | 50 | 0.28 | 0.75 | 13 | empty |
Compared structures
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 3V7L · PDBe 3V7L · UniProt P06766
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