Structure of vacv poxin in pre-reactive state with nonhydrolyzable 2'3' cgamp

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).

Ligands and binding sites

• J2A · (2s,5r,7r,8r,10r,12ar,14r,15r,15as,16r)-7-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-14-(6-amino-9H-purin-9-yl)-15,16-dihydroxy-2,10-disulfanyloctahydro-2H,10H, 12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-L][1, 3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione · ligand · 2 copies · chains A, B, E, F
• J2B · O-[(1R,2R,3R)-5-{[(S)-{[(2R,3R,4R,5R)-2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}(sulfanyl) phosphoryl]oxy}-1-(6-amino-9H-purin-9-yl)-1,2-dihydroxypentan-3-yl] dihydrogen (R)-phosphorothioate · ligand · chains 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, 13 with a druggability of 0.5 or more.

Interfaces

9 interfaces between chains.

• E–F · 1367 Ų buried · 27 hydrogen bonds · protein-protein
• A–B · 1312 Ų buried · 25 hydrogen bonds · protein-protein
• G–H · 1296 Ų buried · 23 hydrogen bonds · protein-protein
• C–D · 1295 Ų buried · 23 hydrogen bonds · protein-protein
• I–J · 1213 Ų buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 6EA8 · Structure of VACV poxin in pre-reactive state with nonhydrolyzable 2'3' cGAMP · the same entry in another collection · chain A against A, 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 Q01225
• Elsewhere: RCSB PDB 6EA8 · PDBe 6EA8 · UniProt Q01225