SMTL ID : 2o07.1

Human spermidine synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 13 residues within 4Å: Chain A: E.25, W.30, V.70, I.71, Q.72, Y.81, Q.82, D.106, D.175, S.176, Y.243, P.244 Ligands: MTA.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.243, A:Y.243 Hydrogen bonds: A:I.71, A:I.71, A:Q.72, A:D.106, A:Y.243 SPD.3: 15 residues within 4Å: Chain B: W.30, V.70, I.71, Q.72, Y.81, Q.82, D.106, D.175, S.176, S.177, D.178, Y.243, P.244, I.248 Ligands: MTA.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Q.72, B:Y.243 Hydrogen bonds: B:Q.72, B:Q.82, B:S.176, B:D.178 Water bridges: B:G.108

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

MTA.2: 20 residues within 4Å: Chain A: Q.51, L.67, Q.72, I.102, G.103, G.104, G.105, D.106, C.125, E.126, I.127, D.128, V.131, G.156, D.157, G.158, D.175, S.176, S.177 Ligands: SPD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.51, A:Q.51, A:G.103, A:G.105, A:I.127, A:D.157, A:D.157, A:G.158, A:S.177 MTA.4: 23 residues within 4Å: Chain B: Q.51, L.67, Q.72, I.102, G.103, G.104, G.105, D.106, C.125, E.126, I.127, D.128, V.131, G.156, D.157, G.158, D.175, S.177, P.182, A.183, S.185, L.186 Ligands: SPD.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.51, B:G.103, B:G.105, B:I.127, B:D.157, B:G.158, B:P.182 Water bridges: B:S.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H. et al., Structure and mechanism of spermidine synthases. Biochemistry (2007)

Release Date

2006-12-12

Peptides

Spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spermidine synthase

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