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RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+ state s1 [t2 dataset]

Analyse RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PBL
Type: protein + DNA
Length: 1,948 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Salmonella typhimurium; Streptococcus thermophilus; SYNTHETIC CONSTRUCT
Molecule: Holliday junction ATP-dependent DNA helicase RuvB; Holliday junction ATP-dependent DNA…
EC: 3.6.4.12
UniProt: A0A2U2MES7, A0A0M0QTS9
Ligands: AGS, ADP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 3.2 · 6 distinct chains · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	Holliday junction ATP-dependent DNA helicase RuvB (EC 3.6.4.12)	protein	312	49% helix, 16% strand	A0A2U2MES7
C	Holliday junction ATP-dependent DNA helicase RuvB (EC 3.6.4.12)	protein	309	50% helix, 15% strand	A0A2U2MES7
D	Holliday junction ATP-dependent DNA helicase RuvB (EC 3.6.4.12)	protein	313	48% helix, 15% strand	A0A2U2MES7
G	Holliday junction ATP-dependent DNA helicase RuvA (EC 3.6.4.12)	protein	48	69% helix, 0% strand	A0A0M0QTS9
U	random DNA sequence	dna	15	—	—
V	random DNA sequence	dna	15	—	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, F, B, C
ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains D, E, F
MG · Magnesium ion · metal · 3 copies · chains A, B, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1191	0.87	0.88	106	AGS, MG
2	1109	0.87	0.89	95	ADP
3	1167	0.87	0.88	103	AGS, MG
4	884	0.86	0.88	83	AGS, MG
5	891	0.86	0.87	113	ADP

Interfaces

18 interfaces between chains.

B–C · 2084 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2003 Å² buried · 20 hydrogen bonds · protein-protein
A–F · 1508 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1427 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1399 Å² buried · 14 hydrogen bonds · protein-protein

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 A0A2U2MES7
Every structure of UniProt A0A0M0QTS9
Elsewhere: RCSB PDB 7PBL · PDBe 7PBL · UniProt A0A2U2MES7 · UniProt A0A0M0QTS9

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