SMTL ID : 6a2d.1

Crystal structure of a synthase 2 from santalum album in complex with ligand1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x 6R2: [bis(chloranyl)-[oxidanyl-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]phosphoryl]methyl]phosphonic acid(Non-covalent)

6R2.1: 19 residues within 4Å: Chain A: S.285, Y.288, A.289, M.292, E.305, G.309, I.312, T.313, D.316, D.320, I.417, F.419, L.422, R.457, N.460, K.476, Y.536 Ligands: MG.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.288, A:Y.288, A:Y.288, A:Y.288, A:A.289, A:I.312, A:I.417, A:F.419, A:L.422 Hydrogen bonds: A:R.457, A:R.457, A:K.476 Water bridges: A:D.316, A:D.316, A:D.316, A:E.394, A:E.394, A:E.394, A:E.394, A:N.460 Halogen bonds: A:N.460 6R2.4: 16 residues within 4Å: Chain B: Q.284, S.285, Y.288, A.289, E.305, G.309, I.312, T.313, D.316, D.320, F.419, L.422, R.457, N.460 Ligands: MG.5, MG.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.288, B:A.289, B:I.312, B:T.313, B:F.419, B:L.422 Hydrogen bonds: B:D.320, B:R.457, B:R.457 Water bridges: B:D.317, B:E.394 Halogen bonds: B:N.460

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.316, D.320 Ligands: 6R2.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.316, A:D.320, H2O.3, H2O.4, H2O.12 MG.3: 4 residues within 4Å: Chain A: D.316, D.320 Ligands: 6R2.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.316, A:D.320, H2O.9, H2O.11 MG.5: 5 residues within 4Å: Chain B: D.316, D.320, E.394 Ligands: 6R2.4, MG.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.316, B:D.320, H2O.23, H2O.25, H2O.28 MG.6: 4 residues within 4Å: Chain B: D.316, D.320 Ligands: 6R2.4, MG.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.316, B:D.320, H2O.24, H2O.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, X. et al., Crystal structure of a synthase 2 from santalum album. To be published

Release Date

2019-06-12

Peptides

Sesquisabinene B synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sesquisabinene B synthase 2

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