SMTL ID : 6hy1.2 (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

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

GXQ.1: 18 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, S.192, I.195, Y.224, P.225, I.229 Ligands: MTA.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.53, A:I.229 Hydrogen bonds: A:Y.62, A:H.63, A:D.159, A:E.191, A:S.192 Water bridges: A:G.89

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 10 PLIP interactions: 10 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:D.138, A:A.139, A:S.158, A:P.163 MTA.8: 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: JFQ.7 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.57, F.60, K.257 Chain B: W.194, F.273 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.257, A:K.257, B:W.194 Water bridges: A:K.57, A:K.57 GOL.5: 7 residues within 4Å: Chain A: Y.97, K.246, K.247, L.248, E.249, S.250, F.253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.247, A:E.249, A:S.250, A:S.250 GOL.6: 5 residues within 4Å: Chain A: I.195, H.196, V.197, G.198, T.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.198 Water bridges: A:I.195, A:V.197 GOL.9: 5 residues within 4Å: Chain A: W.194, F.273 Chain B: K.57, F.60, K.257 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.257, B:K.257 Water bridges: B:K.57, B:K.57 GOL.10: 5 residues within 4Å: Chain B: P.160, F.168, T.199, N.202, Y.206 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.202, B:Y.206, B:Y.206 GOL.11: 10 residues within 4Å: Chain A: F.16, P.222, C.226, G.227 Chain B: F.16, P.222, Y.224, P.225, C.226, G.227 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.222, B:C.226, B:C.226, A:C.226 Water bridges: B:F.16

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

1PG.4: 8 residues within 4Å: Chain A: W.3, S.5, F.7, S.17 Chain B: W.3, S.5, F.7, S.17 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.5, A:S.17, B:W.3, B:S.5

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

JFQ.7: 14 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, Y.224, I.229 Ligands: MTA.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.51, B:Q.53, B:Q.189, B:I.229 Hydrogen bonds: B:H.63, B:D.159, B:Y.224 Water bridges: B:G.88

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
B

B
C

Spermidine synthase

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