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Nucleotide bound form of an isolated E. COLI clamp loader gamma subunit

Analyse Nucleotide bound form of an isolated E. COLI clamp loader gamma subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1358 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 378 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 334 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 256 Å² 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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