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Mechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex

Analyse Mechanistic implications for the bacterial primosome assembly of the structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M4W
Type: protein
Length: 4,043 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replicative helicase; DNA primase; Primosomal protein dnai
UniProt: Q9X4C9, Q9X4D0, P06567
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 19% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Replicative helicase	protein	358	24% helix, 9% strand	Q9X4C9
G, H, I	DNA primase	protein	138	33% helix, 0% strand	Q9X4D0
J	Primosomal protein dnai	protein	245	13% helix, 14% strand	P06567
K	Primosomal protein dnai	protein	248	17% helix, 10% strand	P06567
L	Primosomal protein dnai	protein	247	18% helix, 12% strand	P06567
M	Primosomal protein dnai	protein	247	17% helix, 10% strand	P06567
N	Primosomal protein dnai	protein	244	14% helix, 10% strand	P06567
O	Primosomal protein dnai	protein	250	19% helix, 16% strand	P06567

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	922	0.83	0.85	116	empty
2	1136	0.81	0.82	108	empty
3	129	0.79	0.96	31	empty
4	1199	0.79	0.80	127	empty
5	137	0.78	0.95	24	empty

Interfaces

33 interfaces between chains.

E–F · 1385 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 1319 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 1246 Å² buried · 14 hydrogen bonds · protein-protein
M–N · 1061 Å² buried · 17 hydrogen bonds · protein-protein
L–M · 989 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

4M4W · Mechanistic implications for the bacterial primosome assembly of the structure of a… · the same entry in another collection · chain O against O, TM-score 1.00

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 Q9X4C9
Every structure of UniProt Q9X4D0
Every structure of UniProt P06567
Elsewhere: RCSB PDB 4M4W · PDBe 4M4W · UniProt Q9X4C9 · UniProt Q9X4D0 · UniProt P06567

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