SMTL ID : 6bq4.1

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x ADN: ADENOSINE(Non-covalent)

ADN.1: 17 residues within 4Å: Chain A: Q.57, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, P.190, C.191, L.194 Ligands: B3P.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.57, A:G.111, A:I.133, A:D.134, A:D.163, A:D.163, A:A.164, A:A.183 Water bridges: A:D.132 ADN.4: 16 residues within 4Å: Chain B: Q.57, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, P.190, C.191, L.194 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.57, B:I.133, B:D.134, B:D.163, B:D.163, B:A.164, B:A.183 Water bridges: B:G.111, B:D.132 ADN.7: 17 residues within 4Å: Chain C: Q.57, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, P.190, C.191, L.194 Ligands: B3P.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.57, C:G.111, C:I.133, C:D.134, C:D.163, C:A.164, C:A.183 Water bridges: C:D.132 ADN.10: 16 residues within 4Å: Chain D: Q.57, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, P.190, C.191, L.194 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.57, D:I.133, D:D.134, D:D.163, D:A.164, D:A.183 Water bridges: D:G.111, D:D.132

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.2: 14 residues within 4Å: Chain A: E.33, K.76, L.77, Q.78, Y.87, D.181, L.182, A.183, D.184, Q.217, Y.254, W.258 Ligands: ADN.1, GOL.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.33, A:L.77, A:Q.78, A:Q.78, A:D.184, A:D.184, A:Y.254, A:Y.254 Water bridges: A:K.76, A:K.76, A:D.181, A:D.181 B3P.8: 14 residues within 4Å: Chain C: E.33, K.76, L.77, Q.78, Y.87, D.181, L.182, A.183, D.184, Q.217, Y.254, W.258 Ligands: ADN.7, GOL.9 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.33, C:L.77, C:Q.78, C:Q.78, C:D.184, C:Y.254 Water bridges: C:K.76, C:K.76, C:D.181, C:D.181

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.78, A.183, D.184, W.258 Ligands: B3P.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.78, A:Q.78, A:D.184 Water bridges: A:K.76 GOL.6: 6 residues within 4Å: Chain B: E.33, K.76, L.77, Y.254, W.258 Ligands: MES.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.77 GOL.9: 5 residues within 4Å: Chain C: Q.78, A.183, D.184, W.258 Ligands: B3P.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.78, C:Q.78, C:D.184 Water bridges: C:K.76 GOL.12: 6 residues within 4Å: Chain D: E.33, K.76, L.77, Y.254, W.258 Ligands: MES.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.77

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

MES.5: 10 residues within 4Å: Chain B: Q.78, Y.87, D.181, L.182, A.183, D.184, Q.217, Y.254, W.258 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.78, B:D.184, B:D.184 MES.11: 10 residues within 4Å: Chain D: Q.78, Y.87, D.181, L.182, A.183, D.184, Q.217, Y.254, W.258 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.78, D:D.184, D:D.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekula, B. et al., Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases. Biochem. J. (2018)

Release Date

2018-02-28

Peptides

Thermospermine synthase ACAULIS protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Thermospermine synthase ACAULIS protein

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