SMTL ID : 6j27.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: C.118, C.121 Chain B: C.118, C.121 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.118, A:C.121, B:C.118, B:C.121

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

MTA.2: 17 residues within 4Å: Chain A: F.153, D.154, Q.155, G.185, D.186, D.187, D.207, A.208, D.209, H.232, D.233, L.234, R.235, D.252, V.254, F.263 Ligands: N4P.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.155, A:D.186, A:D.187, A:D.187, A:A.208, A:D.233, A:L.234, A:R.235 pi-Stacking: A:F.263, A:F.263 MTA.6: 16 residues within 4Å: Chain B: F.153, D.154, Q.155, G.185, D.186, D.187, D.207, A.208, D.209, H.232, D.233, L.234, D.252, V.254, F.263 Ligands: N4P.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.155, B:D.186, B:D.187, B:D.187, B:A.208, B:D.233, B:L.234 pi-Stacking: B:F.263, B:F.263

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

N4P.3: 17 residues within 4Å: Chain A: D.154, Q.155, G.156, D.187, D.188, D.252, P.253, E.255, G.281, T.283, E.286, Y.316, W.319, Y.321, Y.342, T.373 Ligands: MTA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.316, A:W.319 Hydrogen bonds: A:D.252, A:D.252, A:E.255, A:Y.321, A:Y.321, A:T.373 Water bridges: A:D.187 Salt bridges: A:D.154, A:D.252 N4P.7: 16 residues within 4Å: Chain B: D.154, Q.155, G.156, D.187, D.188, D.252, P.253, E.255, G.281, T.283, Y.316, W.319, Y.321, Y.342, T.373 Ligands: MTA.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.316, B:W.319 Hydrogen bonds: B:D.252, B:D.252, B:T.373 Water bridges: B:D.187, B:Y.342 Salt bridges: B:D.154, B:D.252

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain A: R.74, R.77, G.312, V.315, T.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.74, A:R.74 Water bridges: A:T.343 PGE.8: 7 residues within 4Å: Chain A: E.274, L.352 Chain B: R.44, P.50, V.51, G.52, A.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.290

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

PEG.5: 6 residues within 4Å: Chain A: P.257, L.260, Q.261, D.294, F.295, F.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.261 Water bridges: A:D.294 PEG.9: 6 residues within 4Å: Chain B: P.257, L.260, K.291, D.294, F.295, F.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.294, B:D.294 PEG.10: 5 residues within 4Å: Chain B: R.74, R.77, G.312, V.315, T.343 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.74, B:R.74 PEG.11: 6 residues within 4Å: Chain A: R.44, L.49, P.50, V.51, G.52 Chain B: E.274 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.274, A:G.48 PEG.12: 4 residues within 4Å: Chain B: A.141, W.142, E.145, R.218 4 PLIP interactions: 4 interactions with chain B Water bridges: B:W.142, B:E.145, B:R.218, B:E.223

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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