SMTL ID : 2o06.1

Human spermidine synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.269, Q.270 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: H.93, D.170, K.200, D.202, G.203 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.93, A:D.170, A:D.202 MG.5: 2 residues within 4Å: Chain B: T.269, Q.270 No protein-ligand interaction detected (PLIP)

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

MTA.3: 20 residues within 4Å: Chain A: Q.51, L.67, Q.72, 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, L.186 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.51, A:G.105, A:I.127, A:G.158, A:P.182 Water bridges: A:S.177 MTA.6: 21 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, L.186 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.51, B:G.105, B:I.127, B:D.157, B:G.158, B:P.182 Water bridges: B:S.177

2 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.4: 12 residues within 4Å: Chain A: W.30, V.70, I.71, Q.72, Y.81, D.175, S.176, S.177, D.178, Y.243, P.244, I.248 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.243 Hydrogen bonds: A:S.176, A:D.178 PUT.7: 12 residues within 4Å: Chain B: W.30, I.71, Q.72, Y.81, D.175, S.176, S.177, D.178, Q.208, Y.243, P.244, I.248 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.243 Hydrogen bonds: B:S.176, B:D.178

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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