Crystal structure of the aminopropyltransferase, spee from hyperthermophilic crenarchaeon, pyrobaculum calidifontis in complex with 5'-methylthioadenosine (mta) alone or together with spermidine or thermospermine

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 31% strand (DSSP).

Ligands and binding sites

• MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
• SPD · Spermidine · ligand · 5 copies · chains A, B, C, D, H
• TER · N-(3-amino-propyl)-N-(5-aminopropyl)-1,4-diaminobutane · ligand · 3 copies · chains E, F, G

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

17 interfaces between chains.

• A–F · 2336 Ų buried · 43 hydrogen bonds · protein-protein
• I–L · 2323 Ų buried · 38 hydrogen bonds · protein-protein
• B–E · 2294 Ų buried · 43 hydrogen bonds · protein-protein
• C–H · 2293 Ų buried · 47 hydrogen bonds · protein-protein
• D–E · 570 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 7XIF · Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic… · the same entry in another collection · chain L against L, 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 A3MU81
• Elsewhere: RCSB PDB 7XIF · PDBe 7XIF · UniProt A3MU81