SMTL ID : 4bp1.2 (1 other biounit)

Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with 5'-Methylthioadenosine and Putrescine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 22 residues within 4Å: Chain A: Q.34, L.50, Q.55, G.86, G.87, D.89, C.108, E.109, I.110, D.111, V.114, E.139, D.140, A.141, D.158, S.159, S.160, P.165, A.166, T.168, L.169 Ligands: PUT.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.34, A:G.86, A:G.87, A:G.88, A:I.110, A:D.140, A:A.141, A:S.160 MTA.4: 22 residues within 4Å: Chain B: Q.34, L.50, Q.55, G.86, G.87, G.88, D.89, C.108, E.109, I.110, D.111, V.114, E.139, D.140, A.141, D.158, S.159, S.160, P.165, A.166, T.168, L.169 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.34, B:Q.34, B:G.86, B:G.88, B:I.110, B:A.141, B:S.160, B:P.165

2 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.2: 10 residues within 4Å: Chain A: V.53, I.54, Q.55, Y.64, D.158, S.159, D.161, Y.226, I.231 Ligands: MTA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.226, A:I.231 Hydrogen bonds: A:Q.55, A:Y.64, A:D.158 Water bridges: A:I.54, A:D.161 PUT.5: 10 residues within 4Å: Chain B: W.13, V.53, I.54, Q.55, Y.64, D.158, S.159, D.161, Y.226, I.231 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.226 Hydrogen bonds: B:S.159, B:D.161

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.59, K.259 Chain B: L.195, W.196, V.199, F.275 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.59, A:K.259, A:K.259 Water bridges: B:W.196

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

1PG.6: 8 residues within 4Å: Chain A: W.5, S.7, F.9, S.19 Chain B: W.5, S.7, F.9, S.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.7, B:S.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sprenger, J. et al., Three-Dimensional Structures of Plasmodium Falciparum Spermidine Synthase with Bound Inhibitors Suggest New Strategies for Drug Design. Acta Crystallogr.,Sect.D (2015)

Release Date

2014-06-04

Peptides

SPERMIDINE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

SPERMIDINE SYNTHASE

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