MolNFT v1 · #11567 · protein
Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. COLI DNA polymerase III: structure of the beta-delta complex
1JQJ · DNA polymerase III, beta chain: “Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. COLI…”. X-ray diffraction, 16 pockets (best druggability 0.49). MolNFT v1 #11567 on GenesisL1: 3D…
- PDB
- 1JQJ
- Type
- protein
- Length
- 1,385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III, beta chain; DNA polymerase III, delta subunit
- EC
- 2.7.7.7
- UniProt
- P0A988, P28630
- Pockets
- 16 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase III, beta chain (EC 2.7.7.7) | protein | 366 | 20% helix, 40% strand | P0A988 |
| C | DNA polymerase III, delta subunit (EC 2.7.7.7) | protein | 328 | 50% helix, 10% strand | P28630 |
| D | DNA polymerase III, delta subunit (EC 2.7.7.7) | protein | 325 | 51% helix, 10% strand | P28630 |
Pockets
16 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.49 | 0.76 | 39 | empty |
| 2 | 197 | 0.49 | 0.76 | 35 | empty |
| 3 | 166 | 0.49 | 0.77 | 24 | empty |
| 4 | 69 | 0.48 | 0.83 | 18 | empty |
| 5 | 158 | 0.46 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 992 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 952 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 82 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1JQJ · Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain A against A, TM-score 0.95
- 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 0.67
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 P0A988
- Every structure of UniProt P28630
- Elsewhere: RCSB PDB 1JQJ · PDBe 1JQJ · UniProt P0A988 · UniProt P28630
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