SMTL ID : 6qmm.1

Crystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.1: 6 residues within 4Å: Chain A: M.54, G.159, S.160, Q.188, Y.223, W.228 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.223 Hydrogen bonds: A:G.159 Water bridges: A:S.160

1 x SPD: SPERMIDINE(Non-covalent)

SPD.2: 12 residues within 4Å: Chain B: W.49, M.50, Y.59, H.60, D.84, D.154, G.155, S.156, D.157, Y.222, W.227 Ligands: MTA.3 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.59, B:W.227 Hydrogen bonds: B:D.84 Water bridges: B:D.157

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

MTA.3: 23 residues within 4Å: Chain B: Q.29, L.43, L.45, M.50, G.81, G.82, G.83, D.84, V.103, E.104, I.105, D.106, V.109, G.134, D.135, G.136, I.137, D.154, G.155, P.161, A.162, L.165 Ligands: SPD.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.29, B:Q.29, B:G.83, B:I.105, B:D.135, B:D.135, B:G.136

1 x PXN: (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol(Non-covalent)

PXN.4: 7 residues within 4Å: Chain B: T.70, A.72, P.180, G.181, D.234, T.235, Q.238 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.180, B:D.234 Hydrogen bonds: B:G.181, B:D.234, B:Q.238 Water bridges: B:Q.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guedez, G. et al., Crystal structure of dimericSynechococcusspermidine synthase with bound polyamine substrate and product. Biochem.J. (2019)

Release Date

2019-03-27

Peptides

Polyamine aminopropyltransferase: A
Polyamine aminopropyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polyamine aminopropyltransferase

Polyamine aminopropyltransferase