Research workbench
Crystal structure of a DNA polymerase III alpha-epsilon chimera
Analyse Crystal structure of a DNA polymerase III alpha-epsilon chimera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GX8
- Type
- protein
- Length
- 1,242 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit EPSILON,DNA polymerase III subunit alpha
- EC
- 2.7.7.7
- UniProt
- P03007, P10443
- Ligands
- CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit EPSILON,DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 306 | 47% helix, 14% strand | P03007, P10443 |
| B, C, D | DNA polymerase III subunit EPSILON,DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 312 | 44% helix, 14% strand | P03007, P10443 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.77 | 0.79 | 125 | empty |
| 2 | 766 | 0.76 | 0.81 | 114 | empty |
| 3 | 376 | 0.61 | 0.77 | 46 | empty |
| 4 | 214 | 0.60 | 0.81 | 29 | empty |
| 5 | 148 | 0.53 | 0.80 | 24 | CL |
Interfaces
4 interfaces between chains.
- C–D · 591 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 381 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GX8 · Crystal structure of a DNA polymerase III alpha-epsilon chimera · the same entry in another collection · chain A against A, TM-score 1.00
- P10443 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit alpha (P10443) · a predicted model of the same protein · chain B against A, TM-score 0.85
- P03007 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit epsilon (P03007) · a predicted model of the same protein · chain D against A, TM-score 0.25
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 P03007
- Every structure of UniProt P10443
- Elsewhere: RCSB PDB 4GX8 · PDBe 4GX8 · UniProt P03007 · UniProt P10443
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