Research workbench

E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4

Analyse E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T22
Type: protein + DNA
Length: 3,097 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.2
Source: Escherichia coli K-12; SYNTHETIC CONSTRUCT
Molecule: Replicative DNA helicase; DNA primase; DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T…
EC: 3.6.4.12, 2.7.7.101
UniProt: P0ACB0, P0ABS5
Ligands: ADP, ALF, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · resolution 4.2 · 3 distinct chains · 57% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Replicative DNA helicase (EC 3.6.4.12)	protein	448	53% helix, 13% strand	P0ACB0
G, H, I	DNA primase (EC 2.7.7.101)	protein	132	70% helix, 0% strand	P0ABS5
M	DNA (5'-D(TPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	dna	13	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E, F
ALF · Tetrafluoroaluminate ion · ligand · 5 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 5 copies · chains B, C, D, E, F

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.81	0.83	136	ADP, ALF, MG
2	793	0.78	0.82	78	empty
3	485	0.75	0.84	56	ADP, ALF, MG
4	527	0.75	0.83	58	ADP, ALF, MG
5	874	0.74	0.79	87	empty

Interfaces

21 interfaces between chains.

B–C · 3591 Å² buried · 45 hydrogen bonds · protein-protein
D–E · 3504 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 2984 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 2904 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2852 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

P0ACB0 · AlphaFold monomer V2.0 prediction for replicative DNA helicase (P0ACB0) · a predicted model of the same protein · chain C against A, TM-score 0.96
P0ABS5 · AlphaFold monomer V2.0 prediction for DNA primase (P0ABS5) · a predicted model of the same protein · chain H against A, TM-score 0.87

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 P0ACB0
Every structure of UniProt P0ABS5
Elsewhere: RCSB PDB 7T22 · PDBe 7T22 · UniProt P0ACB0 · UniProt P0ABS5

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