SMTL ID : 6bq5.1

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with 5'-methylthioadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

B3P.1: 12 residues within 4Å: Chain A: E.33, K.76, L.77, Q.78, Y.87, D.181, L.182, A.183, Q.217, Y.254, W.258 Ligands: MTA.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.33, A:L.77, A:Q.78, A:Q.78, A:D.181, A:Q.217, A:Y.254 Water bridges: A:K.76, A:K.76, A:Q.78, A:Y.254 B3P.5: 13 residues within 4Å: Chain B: E.33, K.76, L.77, Q.78, Y.87, D.181, L.182, A.183, Q.217, Y.254, W.258 Ligands: MTA.6, GOL.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.33, B:Q.78, B:Q.78, B:D.181, B:Q.217 B3P.8: 12 residues within 4Å: Chain C: E.33, K.76, L.77, Q.78, Y.87, D.181, L.182, A.183, Q.217, Y.254, W.258 Ligands: MTA.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:E.33, C:L.77, C:Q.78, C:Q.78, C:Y.87, C:D.181, C:Q.217, C:Y.254, C:Y.254 Water bridges: C:K.76, C:K.76, C:Q.78 B3P.12: 13 residues within 4Å: Chain D: E.33, K.76, L.77, Q.78, Y.87, D.181, L.182, A.183, Q.217, Y.254, W.258 Ligands: MTA.13, GOL.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.33, D:Q.78, D:Q.78, D:D.181, D:Q.217

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

MTA.2: 18 residues within 4Å: Chain A: Q.57, L.73, Q.78, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, C.191, L.194 Ligands: B3P.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.57, A:I.133, A:D.134, A:D.163, A:A.164 Water bridges: A:D.132 MTA.6: 19 residues within 4Å: Chain B: Q.57, L.73, Q.78, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, C.191, L.194 Ligands: B3P.5, GOL.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.57, B:I.133, B:D.134, B:D.163, B:D.163, B:A.164 Water bridges: B:G.110, B:D.132 MTA.9: 18 residues within 4Å: Chain C: Q.57, L.73, Q.78, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, C.191, L.194 Ligands: B3P.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.57, C:I.133, C:D.134, C:D.163, C:D.163, C:A.164 Water bridges: C:D.132 MTA.13: 19 residues within 4Å: Chain D: Q.57, L.73, Q.78, G.109, C.131, D.132, I.133, D.134, V.137, N.162, D.163, A.164, D.181, L.182, A.183, C.191, L.194 Ligands: B3P.12, GOL.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.57, D:I.133, D:D.134, D:D.163, D:A.164 Water bridges: D:G.110, D:D.132

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: K.242 No protein-ligand interaction detected (PLIP) GOL.4: 3 residues within 4Å: Chain A: D.269, S.271, E.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.271 Water bridges: A:D.269 GOL.7: 7 residues within 4Å: Chain B: Q.78, A.183, D.184, Q.217, W.258 Ligands: B3P.5, MTA.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.78, B:Q.78, B:D.184, B:D.184, B:Q.217, B:Q.217 GOL.10: 1 residues within 4Å: Chain C: K.242 No protein-ligand interaction detected (PLIP) GOL.11: 3 residues within 4Å: Chain C: D.269, S.271, E.274 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.271 Water bridges: C:D.269 GOL.14: 7 residues within 4Å: Chain D: Q.78, A.183, D.184, Q.217, W.258 Ligands: B3P.12, MTA.13 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.78, D:Q.78, D:D.184, D:D.184, D:Q.217, D:Q.217

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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