Research workbench
Crystal structure of the processivity clamp loader gamma complex of E. COLI DNA polymerase III
Analyse Crystal structure of the processivity clamp loader gamma complex of E. COLI DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JR3
- Type
- protein
- Length
- 1,769 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit gamma; DNA polymerase III, delta subunit; DNA polymerase III…
- EC
- 2.7.7.7
- UniProt
- P06710, P28630, P28631
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA polymerase III subunit gamma (EC 2.7.7.7) | protein | 366 | 55% helix, 8% strand | P06710 |
| B | DNA polymerase III subunit gamma (EC 2.7.7.7) | protein | 365 | 52% helix, 8% strand | P06710 |
| D | DNA polymerase III, delta subunit (EC 2.7.7.7) | protein | 338 | 54% helix, 11% strand | P28630 |
| E | DNA polymerase III, delta' subunit (EC 2.7.7.7) | protein | 334 | 51% helix, 8% strand | P28631 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, E
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.81 | 0.82 | 115 | empty |
| 2 | 158 | 0.76 | 0.93 | 33 | empty |
| 3 | 568 | 0.73 | 0.81 | 52 | empty |
| 4 | 429 | 0.73 | 0.83 | 46 | empty |
| 5 | 677 | 0.73 | 0.79 | 72 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2762 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1820 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1688 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1644 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 860 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1JR3 · Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA… · the same entry in another collection · chain E against E, TM-score 1.00
- P06710 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit tau (P06710) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P28631 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit delta' (P28631) · a predicted model of the same protein · chain E against A, TM-score 0.91
- P28630 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit delta (P28630) · a predicted model of the same protein · chain D against A, TM-score 0.72
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 P06710
- Every structure of UniProt P28630
- Every structure of UniProt P28631
- Elsewhere: RCSB PDB 1JR3 · PDBe 1JR3 · UniProt P06710 · UniProt P28630 · UniProt P28631
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