SMTL ID : 6j26.1

Crystal structure of the branched-chain polyamine synthase from Thermococcus kodakarensis (Tk-BpsA) in complex with N4-bis(aminopropyl)spermidine and 5'-methylthioadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

MTA.1: 19 residues within 4Å: Chain A: F.145, D.146, Q.147, G.177, D.178, D.179, D.199, I.200, L.204, F.225, D.226, L.227, R.228, D.245, P.247, F.256, L.362, Y.363 Ligands: B5L.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.147, A:D.178, A:D.179, A:D.179, A:I.200, A:D.226, A:L.227, A:Y.363 Water bridges: A:R.228, A:T.244 pi-Stacking: A:F.256, A:F.256 MTA.4: 19 residues within 4Å: Chain B: F.145, D.146, Q.147, G.177, D.178, D.179, D.199, I.200, L.204, F.225, D.226, L.227, R.228, D.245, P.247, F.256, L.362, Y.363 Ligands: B5L.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.147, B:D.178, B:D.179, B:D.179, B:I.200, B:D.226, B:L.227, B:Y.363 Water bridges: B:T.244 pi-Stacking: B:F.256, B:F.256

2 x B5L: N~1~,N~1~,N~1~-tris(3-azaniumylpropyl)butane-1,4-diaminium(Non-covalent)

B5L.2: 19 residues within 4Å: Chain A: D.146, Q.147, A.148, D.179, D.180, D.245, P.246, P.247, E.248, G.274, T.276, E.279, Y.310, W.313, Y.315, Y.336, S.338, T.370 Ligands: MTA.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.148, A:T.276, A:Y.310, A:Y.336 Hydrogen bonds: A:D.146, A:D.245, A:G.274, A:T.370 Water bridges: A:D.179, A:E.248 Salt bridges: A:D.146, A:D.245 B5L.5: 19 residues within 4Å: Chain B: D.146, Q.147, A.148, D.179, D.180, D.245, P.246, P.247, E.248, G.274, T.276, E.279, Y.310, W.313, Y.315, Y.336, S.338, T.370 Ligands: MTA.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.148, B:E.248, B:T.276, B:Y.310, B:Y.336 Hydrogen bonds: B:D.180, B:G.274, B:E.279, B:T.370 Water bridges: B:E.248 Salt bridges: B:D.146, B:D.245

1 x FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain A: C.111, C.114 Chain B: C.111, C.114 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.111, B:C.114, A:C.111, A:C.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hidese, R. et al., The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis. Febs J. (2019)

Release Date

2019-06-26

Peptides

N(4)-bis(aminopropyl)spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N(4)-bis(aminopropyl)spermidine synthase

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