SMTL ID : 6j28.2 (1 other biounit)

Crystal structure of the branched-chain polyamine synthase C9 mutein from Thermus thermophilus (Tth-BpsA C9) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

N4P.1: 15 residues within 4Å: Chain A: D.154, Q.155, G.156, D.187, D.188, D.252, P.253, E.255, E.286, Y.316, W.319, Y.321, Y.342, T.374 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:E.255, A:E.255, A:Y.321, A:T.374, A:T.374 Water bridges: A:D.187 Salt bridges: A:D.154, A:D.252 N4P.5: 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.374 Ligands: MTA.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.283, B:Y.316, B:W.319 Hydrogen bonds: B:D.252, B:G.281, B:T.374 Water bridges: B:D.187 Salt bridges: B:D.154, B:D.252

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

MTA.2: 18 residues within 4Å: Chain A: F.153, D.154, Q.155, G.185, D.186, D.187, D.207, A.208, H.232, D.233, L.234, R.235, D.252, V.254, F.263, L.366, Y.367 Ligands: N4P.1 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 pi-Stacking: A:F.153, A:F.263, A:F.263 MTA.6: 18 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, R.235, D.252, V.254, F.263, Y.367 Ligands: N4P.5 10 PLIP interactions: 10 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, B:Y.367 pi-Stacking: B:F.263, B:F.263

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

FE.3: 4 residues within 4Å: Chain A: C.118, C.121 Chain B: C.118, C.121 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.118, B:C.121, A:C.118, A:C.121

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 4 residues within 4Å: Chain A: E.317, N.318, E.338, K.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.318 Salt bridges: A:E.317 MES.7: 8 residues within 4Å: Chain A: N.172 Chain B: R.74, L.75, R.77, P.113, G.114, G.312, T.343 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.74 Water bridges: B:D.311, B:G.312, B:T.343 Salt bridges: B:R.74

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
B

B
D

N(4)-bis(aminopropyl)spermidine synthase

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