Legionella pneumophila NTPDASE1 crystal form II (closed) in complex with heptamolybdate and octamolybdate

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).

Ligands and binding sites

• M27 · bis(mu2-oxo)-octaoxo-dimolybdenum (VI) · ligand · 4 copies · chains A, B
• 6LL · Tetrakis-(mu-oxo)-deca-oxo-trimolybdenum · ligand · 2 copies · chains A, B
• MO7 · bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI) · ligand · 2 copies · chains A, B
• 8M0 · bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 5 copies · chains A, B
• NA · Sodium ion · metal · chains A, B
• MOO · Molybdate ion · ion · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• GOL · Glycerol · additive · 7 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1539 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 4BVP · Legionella pneumophila NTPDase1 crystal form II (closed) in complex with heptamolybdate… · 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 Q5ZUA2
• Elsewhere: RCSB PDB 4BVP · PDBe 4BVP · UniProt Q5ZUA2