SMTL ID : 5xnc.4 (3 other biounits)

Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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: N4P.2 11 PLIP interactions: 11 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:D.226, A:L.227, A:Y.363 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: N4P.5 9 PLIP interactions: 9 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 pi-Stacking: B:F.256, B:F.256

2 x N4P: N,N-bis(3-aminopropyl)butane-1,4-diamine(Non-covalent)

N4P.2: 15 residues within 4Å: Chain A: D.146, A.148, D.179, D.180, D.245, P.246, E.248, G.274, I.275, Y.310, W.313, Y.315, Y.336, T.370 Ligands: MTA.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.148 Hydrogen bonds: A:D.146, A:D.180, A:G.274, A:T.370, A:T.370 Water bridges: A:D.179 Salt bridges: A:D.146, A:D.245 N4P.5: 15 residues within 4Å: Chain B: D.146, A.148, D.179, D.180, D.245, P.246, E.248, G.274, I.275, Y.310, W.313, Y.315, Y.336, T.370 Ligands: MTA.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.148 Hydrogen bonds: B:D.180, B:D.245, B:E.248, B:G.274, B:Y.315, B:T.370 Water bridges: B:D.179 Salt bridges: B:D.146, B:D.245

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

FE.3: 5 residues within 4Å: Chain A: C.111, C.114 Chain B: C.111, C.114 Ligands: FE.6 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 FE.6: 5 residues within 4Å: Chain A: C.111, C.114 Chain B: C.111, C.114 Ligands: FE.3 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., Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine. FEBS J. (2017)

Release Date

2018-08-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
G

N(4)-bis(aminopropyl)spermidine synthase

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