SMTL ID : 6hy1.1 (1 other biounit)

Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x GXQ: N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine(Non-covalent)

GXQ.1: 16 residues within 4Å: Chain A: W.11, V.51, I.52, Q.53, Y.62, H.63, D.87, D.156, S.157, D.159, Q.189, E.191, Y.224, P.225, I.229 Ligands: MTA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.51, A:Y.62, A:Q.189, A:Y.224, A:I.229 Hydrogen bonds: A:D.87, A:S.157, A:Q.189, A:E.191 Water bridges: A:I.52, A:G.88 GXQ.5: 16 residues within 4Å: Chain B: W.11, V.51, I.52, Q.53, Y.62, H.63, D.87, D.156, S.157, D.159, Q.189, E.191, Y.224, P.225, I.229 Ligands: MTA.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.51, B:Y.62, B:Q.189, B:Y.224, B:I.229 Hydrogen bonds: B:D.87, B:S.157, B:Q.189, B:E.191, B:E.191 Water bridges: B:I.52, B:G.88

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

MTA.2: 23 residues within 4Å: Chain A: Q.32, L.48, Q.53, G.84, G.85, G.86, D.87, C.106, E.107, I.108, D.109, V.112, E.137, D.138, A.139, D.156, S.157, S.158, P.163, A.164, T.166, L.167 Ligands: GXQ.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.32, A:Q.32, A:G.84, A:G.85, A:G.86, A:I.108, A:A.139, A:S.158, A:P.163 MTA.6: 23 residues within 4Å: Chain B: Q.32, L.48, Q.53, G.84, G.85, G.86, D.87, C.106, E.107, I.108, D.109, V.112, E.137, D.138, A.139, D.156, S.157, S.158, P.163, A.164, T.166, L.167 Ligands: GXQ.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.32, B:Q.32, B:G.84, B:G.85, B:G.86, B:I.108, B:D.138, B:A.139, B:S.158, B:P.163

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

1PG.3: 9 residues within 4Å: Chain A: W.3, S.5, F.7, S.17 Chain B: W.3, S.5, F.7, S.17 Ligands: 1PG.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.5, B:S.17 1PG.7: 9 residues within 4Å: Chain A: W.3, S.5, F.7, S.17 Chain B: W.3, S.5, F.7, S.17 Ligands: 1PG.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.5, A:S.17

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: K.57, F.60 Chain B: W.194, F.273 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.194 GOL.8: 4 residues within 4Å: Chain A: W.194, F.273 Chain B: K.57, F.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sprenger, J. et al., Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N,N'-Bis(3-aminopropyl)-1,4-cyclohexanediamine after catalysis in crystal. To Be Published

Release Date

2019-10-30

Peptides

Spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Spermidine synthase

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