Cryoem structure of the complete E. COLI DNA gyrase complex bound to a 130 bp DNA duplex

Structure

electron microscopy · 4 distinct chains · 34% helix, 21% strand (DSSP).

Ligands and binding sites

• ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, D
• JHN · (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione · ligand · chains A, C, G, H

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.

Interfaces

25 interfaces between chains.

• B–D · 3066 Ų buried · 37 hydrogen bonds · protein-protein
• E–G · 2673 Ų buried · 223 hydrogen bonds · nucleic-nucleic
• F–H · 2589 Ų buried · 175 hydrogen bonds · nucleic-nucleic
• A–B · 1474 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 1448 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 6RKW · CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex · the same entry in another collection · chain H against H, TM-score 1.00
• P0AES4 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES4) · a predicted model of the same protein · chain C against A, TM-score 0.69
• P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain D against A, TM-score 0.50

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 P0AES4
• Every structure of UniProt P0AES6
• Elsewhere: RCSB PDB 6RKW · PDBe 6RKW · UniProt P0AES4 · UniProt P0AES6