SMTL ID : 4bp3.2 (1 other biounit)

Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with DECARBOXYLATED S-ADENOSYLMETHIONINE5' AND 4- METHYLANILINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x 4MN: 4-METHYLANILINE(Non-covalent)

4MN.1: 13 residues within 4Å: Chain A: W.13, V.53, I.54, Q.55, Y.64, D.158, S.159, D.161, Q.191, Y.226, P.227, I.231 Ligands: S4M.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.53, A:Q.191, A:I.231 Hydrogen bonds: A:D.161 pi-Stacking: A:Y.226 4MN.4: 13 residues within 4Å: Chain B: W.13, V.53, I.54, Q.55, Y.64, D.158, S.159, D.161, Q.191, Y.226, P.227, I.231 Ligands: S4M.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.53, B:I.231 Hydrogen bonds: B:D.161 pi-Stacking: B:Y.226

2 x S4M: 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE(Non-covalent)

S4M.2: 25 residues within 4Å: Chain A: Q.34, L.50, Q.55, Y.64, H.65, 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, Y.226 Ligands: 4MN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.55 Hydrogen bonds: A:Q.34, A:H.65, A:G.86, A:I.110, A:D.140, A:A.141, A:S.160 Water bridges: A:G.90 Salt bridges: A:D.89, A:D.158 S4M.5: 26 residues within 4Å: Chain B: Q.34, L.50, Q.55, Y.64, H.65, 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, Y.226 Ligands: 4MN.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Q.55 Hydrogen bonds: B:Q.34, B:H.65, B:G.86, B:G.88, B:I.110, B:D.140, B:A.141, B:S.160, B:P.165 Water bridges: B:G.90 Salt bridges: B:D.89, B:D.158

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.59, F.62 Chain B: L.195, W.196, V.199, F.275 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:V.199, A:K.59 Hydrogen bonds: A:K.59

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

1PG.6: 12 residues within 4Å: Chain A: N.220, S.222, Y.260, A.268, A.269, K.271 Chain B: N.220, A.268, A.269, K.271, L.272, P.273 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.220, B:N.220 Water bridges: A:Y.260 1PG.7: 8 residues within 4Å: Chain A: W.5, S.7, F.9, S.19 Chain B: W.5, S.7, F.9, S.19 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.7, A:S.19, 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

2014-06-25

Peptides

SPERMIDINE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

SPERMIDINE SYNTHASE

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