Crystal structure of the branched-chain polyamine synthase (bpsa) in complex with N4-aminopropylspermidine and 5-methylthioadenosine

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).

Ligands and binding sites

• MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 7 copies · chains A, B, C, D, E, F, G
• N4P · N,N-bis(3-aminopropyl)butane-1,4-diamine · ligand · 7 copies · chains A, B, C, D, E, F, G
• FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D, E, F, G
• GOL · Glycerol · additive · 5 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 3 copies · chains C, D, E
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, E

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 2528 Ų buried · 47 hydrogen bonds · protein-protein
• E–F · 2490 Ų buried · 40 hydrogen bonds · protein-protein
• C–D · 2465 Ų buried · 46 hydrogen bonds · protein-protein
• C–E · 382 Ų buried · 16 hydrogen bonds · protein-protein
• B–C · 361 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 5XNC · Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with… · the same entry in another collection · chain G against G, TM-score 1.00
• Q5JIZ3 · AlphaFold monomer V2.0 prediction for N(4)-BIS(AMINOPROPYL)SPERMIDINE synthase (Q5JIZ3) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q5JIZ3
• Elsewhere: RCSB PDB 5XNC · PDBe 5XNC · UniProt Q5JIZ3