MolNFT v1 · #15922 · protein
Nucleotide bound form of an isolated E. COLI clamp loader gamma subunit
1NJF · DNA polymerase III subunit gamma: “Nucleotide bound form of an isolated E. COLI clamp loader gamma subunit”. X-ray diffraction, 3 ligands (AGS, ADP, ZN), 8 pockets (best druggability 0.83). MolNFT v1 #15922 on GenesisL1: 3D…
- PDB
- 1NJF
- Type
- protein
- Length
- 956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit gamma
- EC
- 2.7.7.7
- UniProt
- P06710
- Ligands
- AGS, ADP, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA polymerase III subunit gamma (EC 2.7.7.7) | protein | 239 | 49% helix, 12% strand | P06710 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · chains C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.83 | 0.88 | 86 | AGS |
| 2 | 1112 | 0.81 | 0.82 | 123 | AGS |
| 3 | 408 | 0.74 | 0.84 | 40 | empty |
| 4 | 220 | 0.74 | 0.89 | 38 | AGS |
| 5 | 296 | 0.70 | 0.84 | 37 | ADP |
Interfaces
5 interfaces between chains.
- A–B · 1436 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1358 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 378 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 256 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1NJF · Nucleotide bound form of an isolated E. coli clamp loader gamma subunit · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 1NJF · PDBe 1NJF · UniProt P06710
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