SMTL ID : 3rie.2 (1 other biounit)

The structure of Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N-(3-aminopropyl)-trans-cyclohexane-1,4-diamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

MTA.1: 23 residues within 4Å: Chain A: 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 Ligands: JFQ.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.34, 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.5: 23 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 Ligands: JFQ.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.34, B:Q.34, B:G.86, B:I.110, B:D.140, B:A.141, B:S.160

2 x JFQ: trans-N-(3-aminopropyl)cyclohexane-1,4-diamine(Non-covalent)

JFQ.2: 13 residues within 4Å: Chain A: V.53, I.54, Q.55, Y.64, H.65, D.89, D.158, S.159, D.161, Q.191, Y.226, I.231 Ligands: MTA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.53, A:Q.55, A:I.231 Hydrogen bonds: A:Y.64, A:H.65, A:D.161 Water bridges: A:G.90 JFQ.6: 14 residues within 4Å: Chain B: W.13, V.53, I.54, Q.55, Y.64, H.65, D.89, D.158, S.159, D.161, Q.191, Y.226, I.231 Ligands: MTA.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.53, B:Q.55, B:Y.226, B:Y.226, B:I.231 Hydrogen bonds: B:H.65, B:Y.226 Water bridges: B:I.54, B:G.90, B:D.161, B:E.193

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.59, F.62, K.259 Chain B: W.196, F.275 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:W.196, A:K.259, A:K.259 Water bridges: A:K.59 GOL.7: 4 residues within 4Å: Chain A: W.196, F.275 Chain B: K.59, F.62 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.59, B:K.59, B:K.59

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burger, P.B. et al., A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail. Malar J (2015)

Release Date

2012-04-25

Peptides

Spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Spermidine synthase

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