SMTL ID : 8x35.1

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.88, R.139 Ligands: IPE.2, DST.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.88, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.88, R.139 Ligands: DPO.7, DPO.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.88, H2O.3

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

IPE.2: 18 residues within 4Å: Chain A: I.86, M.87, D.88, F.130, A.131, F.132, S.133, N.136, R.139, R.251, R.257, S.259 Chain B: Y.268, R.299, F.300, G.301 Ligands: MG.1, DST.3 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.86, A:F.130, A:F.130 Hydrogen bonds: A:N.136, A:S.259, A:S.259, B:G.301 Water bridges: A:R.139, A:R.139, A:R.251, B:Y.268, B:R.299, B:R.299, B:R.299, B:F.300 Salt bridges: A:R.139, A:R.251, A:R.251, A:R.257

1 x DST: DIMETHYLALLYL S-THIOLODIPHOSPHATE(Non-covalent)

DST.3: 15 residues within 4Å: Chain A: M.87, D.88, G.89, N.90, R.91, R.92, H.105, A.131, N.136, R.139, L.147 Chain B: R.299, H.303 Ligands: MG.1, IPE.2 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.147 Hydrogen bonds: A:G.89, A:N.90, A:R.91, A:R.92, A:R.139, A:R.139 Salt bridges: A:R.92, B:R.299 Water bridges: B:R.299, B:R.299, B:R.299

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 8 residues within 4Å: Chain A: H.82, I.126, T.128, V.198, S.241, K.242, C.243, P.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.128, A:C.243 Water bridges: A:K.242, A:K.242

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: Q.256 Chain B: Y.272, F.273, N.292, R.296 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.273, B:N.292, B:N.292, B:R.296, A:Q.256 Water bridges: B:Q.256, A:Q.256

2 x DPO: DIPHOSPHATE(Non-covalent)

DPO.7: 9 residues within 4Å: Chain B: D.88, N.136, R.139, R.251, E.255, R.257, S.259 Ligands: MG.6, DPO.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.136, B:E.255, B:E.255, B:E.255, B:S.259 Salt bridges: B:R.139, B:R.251, B:R.257 DPO.8: 10 residues within 4Å: Chain B: M.87, D.88, G.89, N.90, R.91, R.92, H.105, R.139 Ligands: MG.6, DPO.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.88, B:G.89, B:N.90, B:N.90, B:R.91, B:R.92 Salt bridges: B:R.91, B:R.91, B:R.92, B:H.105, B:R.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imaizumi, R. et al., Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato. Chembiochem (2024)

Release Date

2024-02-07

Peptides

Neryl diphosphate synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neryl diphosphate synthase 1