SMTL ID : 6o64.3 (3 other biounits)

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 6 residues within 4Å: Chain A: W.233, T.234, S.235 Chain B: S.235, V.243, A.288 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.233 Water bridges: B:W.233 MLI.3: 5 residues within 4Å: Chain A: E.120, I.121, G.150, D.151, G.152 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.121, A:D.151, A:G.152, A:V.153 Water bridges: A:G.98, A:S.172

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: L.67, Q.76, G.98, G.99, D.100, G.101, G.102, V.103, L.104 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.76, A:D.100, A:D.100, A:G.101, A:G.101, A:G.102, A:V.103, A:L.104

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 12 residues within 4Å: Chain A: W.24, V.64, I.65, Q.66, Y.75, D.170, S.171, D.173, Q.203, Y.239, P.240, I.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.170, A:Y.239 Water bridges: A:D.173, A:E.205 PEG.8: 10 residues within 4Å: Chain B: V.64, I.65, Q.66, Y.75, D.170, S.171, D.173, Q.203, Y.239, P.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.75, B:D.170 Water bridges: B:D.173 PEG.9: 3 residues within 4Å: Chain B: K.91, E.114, D.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.114, B:D.165

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 2 residues within 4Å: Chain A: F.295 Chain B: C.73 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.279 FMT.6: 4 residues within 4Å: Chain A: N.230, Y.231, F.290, L.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.231, A:F.290

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: S.287, A.288, C.291 Chain B: S.287, A.288 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.288 Water bridges: B:E.284, B:S.287, A:S.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekula, B. et al., Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms FromArabidopsis thaliana. Front Plant Sci (2019)

Release Date

2019-06-05

Peptides

Spermidine synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Spermidine synthase 2

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