MolNFT v1 · #27896 · protein
ADP bound E. COLI clamp loader complex
1XXI · DNA polymerase III, delta subunit: “ADP bound E. COLI clamp loader complex”. X-ray diffraction, 3 ligands (ADP, ZN, PO4), 20 pockets (best druggability 0.83). MolNFT v1 #27896 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1XXI
- Type
- protein
- Length
- 3,532 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III, delta subunit; DNA polymerase III subunit gamma; DNA polymerase III…
- EC
- 2.7.7.7
- UniProt
- P28630, P06710, P28631
- Ligands
- ADP, ZN, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DNA polymerase III, delta subunit (EC 2.7.7.7) | protein | 338 | 53% helix, 11% strand | P28630 |
| B, D, G, I | DNA polymerase III subunit gamma (EC 2.7.7.7) | protein | 364 | 55% helix, 8% strand | P06710 |
| C, H | DNA polymerase III subunit gamma (EC 2.7.7.7) | protein | 366 | 55% helix, 8% strand | P06710 |
| E, J | DNA polymerase III, delta prime subunit (EC 2.7.7.7) | protein | 334 | 51% helix, 8% strand | P28631 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains D, B, I
- ZN · Zinc ion · metal · 8 copies · chains C, D, B, E, H, I, G, J
- PO4 · Phosphate ion · ion · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.83 | 0.84 | 128 | PO4 |
| 2 | 1000 | 0.80 | 0.81 | 92 | empty |
| 3 | 1029 | 0.80 | 0.81 | 95 | empty |
| 4 | 156 | 0.78 | 0.95 | 28 | empty |
| 5 | 1018 | 0.78 | 0.80 | 112 | ADP |
Interfaces
17 interfaces between chains.
- H–I · 2617 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2598 Ų buried · 33 hydrogen bonds · protein-protein
- I–J · 1983 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1957 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1669 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
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 P28630
- Every structure of UniProt P06710
- Every structure of UniProt P28631
- Elsewhere: RCSB PDB 1XXI · PDBe 1XXI · UniProt P28630 · UniProt P06710 · UniProt P28631
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