Research workbench
Eubacterial and eukaryotic replicative DNA polymerases are not homologous: X-ray structure of DNA polymerase III
Analyse Eubacterial and eukaryotic replicative DNA polymerases are not homologous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HPM
- Type
- protein
- Length
- 1,143 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III alpha subunit
- EC
- 2.7.7.7
- UniProt
- Q9XDH5
- Ligands
- 3PO, ZN, MG, CL
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III alpha subunit (EC 2.7.7.7) | protein | 1143 | 45% helix, 15% strand | Q9XDH5 |
Ligands and binding sites
- 3PO · Triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.60 | 0.81 | 38 | empty |
| 2 | 345 | 0.60 | 0.77 | 39 | empty |
| 3 | 79 | 0.52 | 0.84 | 16 | empty |
| 4 | 172 | 0.52 | 0.78 | 20 | empty |
| 5 | 176 | 0.52 | 0.79 | 23 | empty |
Compared structures
- 2HPM · Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XDH5 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit alpha (Q9XDH5) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 Q9XDH5
- Elsewhere: RCSB PDB 2HPM · PDBe 2HPM · UniProt Q9XDH5
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