SMTL ID : 2i7c.1 (1 other biounit)

The crystal structure of spermidine synthase from p. falciparum in complex with AdoDATO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x AAT: S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE(Non-covalent)

AAT.1: 28 residues within 4Å: Chain A: W.13, Q.34, L.50, V.53, Q.55, Y.64, H.65, G.86, G.87, D.89, C.108, E.109, I.110, V.114, E.139, D.140, A.141, D.158, S.159, S.160, D.161, P.165, A.166, T.168, L.169, Y.226, P.227, I.231 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.226 Hydrogen bonds: A:Q.34, A:H.65, A:G.86, A:G.87, A:G.88, A:I.110, A:D.140, A:D.140, A:A.141, A:S.160, A:D.161 Water bridges: A:D.89 AAT.4: 28 residues within 4Å: Chain B: W.13, Q.34, L.50, V.53, Q.55, Y.64, H.65, G.86, G.87, D.89, C.108, E.109, I.110, V.114, E.139, D.140, A.141, D.158, S.159, S.160, D.161, P.165, A.166, T.168, L.169, Y.226, P.227, I.231 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.226 Hydrogen bonds: B:Q.34, B:H.65, B:G.86, B:G.87, B:G.88, B:I.110, B:D.140, B:A.141, B:S.160, B:D.161 Water bridges: B:D.89

2 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.2: 9 residues within 4Å: Chain A: W.5, S.7, F.9, S.19 Chain B: W.5, S.7, F.9, S.19 Ligands: 1PG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.7, A:S.19 1PG.5: 9 residues within 4Å: Chain A: W.5, S.7, F.9, S.19 Chain B: W.5, S.7, F.9, S.19 Ligands: 1PG.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.7, B:S.19

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.59, F.62 Chain B: W.196, F.275 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.196 GOL.6: 4 residues within 4Å: Chain A: W.196, F.275 Chain B: K.59, F.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dufe, V.T. et al., Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO. J.Mol.Biol. (2007)

Release Date

2006-09-12

Peptides

Spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Spermidine synthase

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