SMTL ID : 2pt6.2 (1 other biounit)

The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

S4M.1: 24 residues within 4Å: Chain A: Q.72, L.88, Q.93, Y.102, H.103, G.124, G.125, D.127, C.146, E.147, I.148, D.149, V.152, E.177, D.178, A.179, D.196, S.197, S.198, P.203, A.204, T.206, L.207, Y.264 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.93 Hydrogen bonds: A:Q.72, A:G.124, A:G.125, A:D.127, A:I.148, A:D.178, A:A.179, A:S.198 Water bridges: A:G.128 Salt bridges: A:D.127, A:D.196 S4M.3: 25 residues within 4Å: Chain B: Q.72, L.86, L.88, Q.93, Y.102, H.103, G.124, G.125, D.127, C.146, E.147, I.148, D.149, V.152, E.177, D.178, A.179, D.196, S.197, S.198, P.203, A.204, T.206, L.207, Y.264 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.72, B:H.103, B:G.124, B:G.125, B:G.126, B:I.148, B:D.178, B:D.178, B:A.179, B:S.198 Water bridges: B:G.129 Salt bridges: B:D.127, B:D.196

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: K.97, F.100 Chain B: W.234, F.313 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.234 Water bridges: B:W.234 GOL.5: 4 residues within 4Å: Chain A: W.234, F.313 Chain B: K.97, F.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.234

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

1PG.4: 9 residues within 4Å: Chain A: K.42, W.43, S.45, F.47, S.57 Chain B: W.43, S.45, F.47, S.57 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.42, A:S.45, A:S.57, B:S.45

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

2008-04-01

Peptides

Spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Spermidine synthase

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