SMTL ID : 8kgb.2 (1 other biounit)

SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

2 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.1: 17 residues within 4Å: Chain A: I.42, M.43, D.44, F.86, F.88, S.89, N.92, R.95, R.211, R.217, S.219 Chain B: Y.228, R.259, F.260, G.261 Ligands: GST.2, MG.3 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.42, A:F.86 Hydrogen bonds: A:N.92, A:S.219, B:R.259, B:R.259, B:F.260, B:G.261 Water bridges: A:R.95, A:R.95, A:R.95, A:R.211, A:R.211, B:R.259 Salt bridges: A:R.95, A:R.211, A:R.211, A:R.217 IPE.5: 16 residues within 4Å: Chain A: Y.228, R.259, F.260, G.261 Chain B: I.42, M.43, D.44, F.86, S.89, N.92, R.95, R.211, R.217, S.219 Ligands: MG.4, GST.6 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.86, B:F.86 Hydrogen bonds: B:N.92, B:S.219, A:R.259, A:F.260, A:G.261 Water bridges: B:R.95, B:R.95, B:R.211, B:R.211, A:Y.228, A:R.259, A:R.259 Salt bridges: B:R.95, B:R.211, B:R.211, B:R.217

2 x GST: GERANYL S-THIOLODIPHOSPHATE(Non-covalent)

GST.2: 16 residues within 4Å: Chain A: M.43, D.44, G.45, N.46, R.47, R.48, H.61, I.64, A.87, F.88, N.92, R.95, L.103 Chain B: H.263 Ligands: IPE.1, MG.3 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.64, A:F.88, A:L.103, A:L.103 Hydrogen bonds: A:G.45, A:N.46, A:R.47, A:R.48, A:R.95, A:R.95, B:H.263 Salt bridges: A:R.48, B:R.259, B:H.263 Water bridges: B:R.259, B:R.259, B:R.259 GST.6: 20 residues within 4Å: Chain A: R.259, H.263 Chain B: M.43, D.44, G.45, N.46, R.47, R.48, H.61, I.64, A.87, F.88, N.92, R.95, V.100, L.103, L.104, F.107 Ligands: MG.4, IPE.5 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Water bridges: A:R.259, A:R.259, A:R.259 Salt bridges: A:H.263, B:R.48 Hydrophobic interactions: B:I.64, B:F.88, B:F.88, B:L.103, B:L.103, B:L.104, B:F.107 Hydrogen bonds: B:G.45, B:N.46, B:R.47, B:R.48, B:R.95, B:R.95

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.44 Ligands: IPE.1, GST.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.44, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain A: R.259 Chain B: D.44, R.48 Ligands: IPE.5, GST.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.44, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suenaga-Hiromori, M. et al., A versatile system for enzymatic synthesis of natural and unnatural polyisoprenoids on rubber particles. To Be Published

Release Date

2024-08-21

Peptides

Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2

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