SMTL ID : 2e5w.2 (1 other biounit)

Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: Y.14, Y.199, L.200, A.230, S.231 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.14, A:L.200 Hydrogen bonds: A:S.197 Water bridges: A:Y.14, A:Y.14, A:Y.199, B:G.228 ACT.4: 3 residues within 4Å: Chain B: Y.14, Y.199, S.231 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:V.226, A:G.228 Hydrophobic interactions: B:Y.14 Hydrogen bonds: B:S.197

1 x AG3: 1-{4-[(3-aminopropyl)amino]butyl}guanidine(Non-covalent)

AG3.2: 16 residues within 4Å: Chain A: E.8, Y.10, T.51, V.52, Q.53, Y.62, H.63, D.87, D.161, S.162, D.164, Q.194, F.201, Y.229, W.233 Ligands: MTA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.53, A:Q.194 Hydrogen bonds: A:Y.10, A:Y.10, A:Y.10, A:Q.53, A:H.63 Water bridges: A:Q.53, A:G.89 Salt bridges: A:E.8, A:D.164 pi-Cation interactions: A:Y.229

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

MTA.3: 23 residues within 4Å: Chain A: Q.32, I.48, Q.53, I.83, G.84, G.85, G.86, D.87, V.106, E.107, I.108, D.109, V.112, G.143, D.144, G.145, D.161, S.162, T.163, P.168, A.169, L.172 Ligands: AG3.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.32, A:Q.32, A:I.108, A:D.144, A:D.144, A:G.145, A:T.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, H. et al., Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3. To be Published

Release Date

2007-06-26

Peptides

Probable spermidine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Probable spermidine synthase

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