SMTL ID : 4yv0.2 (1 other biounit)

Crystal structure of Trypanosoma cruzi spermidine synthase in complex with (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine- 2-carboxamid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x S4M: 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE(Non-covalent)

S4M.1: 21 residues within 4Å: Chain A: Q.48, M.65, L.67, Q.72, Y.81, H.82, I.102, G.103, G.104, D.106, V.125, D.126, I.127, D.128, V.131, G.156, D.157, G.158, D.176, T.177, T.178 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.72 Hydrogen bonds: A:Q.48, A:H.82, A:I.127, A:D.128, A:D.157, A:G.158, A:T.178 Water bridges: A:G.108 Salt bridges: A:D.106, A:D.176 S4M.2: 23 residues within 4Å: Chain B: Q.48, M.65, L.67, Q.72, Y.81, H.82, I.102, G.103, D.106, V.125, D.126, I.127, D.128, V.131, G.156, D.157, G.158, D.176, T.177, T.178, P.183, A.184, L.187 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.72 Hydrogen bonds: B:Q.48, B:H.82, B:G.105, B:I.127, B:D.157, B:G.158, B:T.178, B:P.183 Water bridges: B:G.108 Salt bridges: B:D.106, B:D.176

1 x 4JW: (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide(Non-covalent)

4JW.3: 17 residues within 4Å: Chain A: E.22, M.32, S.33, L.34, W.61, I.71, P.243, T.244 Chain B: E.22, W.27, Q.30, A.31, M.32, T.244, Y.245, P.246, C.247 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:M.32, A:L.34, A:L.34, A:I.71, B:W.27, B:M.32, B:P.246 Hydrogen bonds: B:C.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amano, Y. et al., Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-09-16

Peptides

Spermidine synthase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Spermidine synthase, putative

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