SMTL ID : 6o63.1 (1 other biounit)

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 11 residues within 4Å: Chain A: W.58, V.98, I.99, Q.100, Y.109, D.204, S.205, D.207, Y.273, P.274, I.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.109, A:D.204, A:Y.273 Water bridges: A:D.207 PEG.3: 12 residues within 4Å: Chain B: W.58, V.98, I.99, Q.100, Y.109, D.204, S.205, D.207, Q.237, Y.273, P.274, I.278 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.204, B:Y.273 Water bridges: B:D.207

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.104, K.311 Chain B: W.242, F.327 No protein-ligand interaction detected (PLIP) GOL.4: 9 residues within 4Å: Chain B: I.130, G.131, E.154, I.155, G.184, D.185, G.186, P.211, L.215 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.154, B:I.155, B:D.185, B:G.186 Water bridges: B:Q.79, B:G.132, B:G.132

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain B: R.143, H.144, A.145, S.146, I.299 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.145, B:S.146 Water bridges: B:H.144, B:S.146, B:S.146, B:N.297, B:N.297

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 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spermidine synthase 1

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