SMTL ID : 3p5p.1

Crystal Structure of Taxadiene Synthase from Pacific Yew (Taxus brevifolia) in complex with Mg2+ and 13-aza-13,14-dihydrocopalyl diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 4 residues within 4Å: Chain A: N.651, T.655, E.659 Ligands: A3C.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.655, A:E.659, H2O.1 MG.2: 3 residues within 4Å: Chain A: D.507, D.511 Ligands: A3C.4 No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x A3C: 2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate(Non-covalent)

A3C.4: 18 residues within 4Å: Chain A: V.478, S.481, F.496, G.500, Q.503, V.504, D.507, V.608, C.613, W.647, R.648, N.651, T.655, E.659, V.725, Y.729 Ligands: MG.1, MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.478, A:Q.503, A:V.504, A:V.608, A:W.647 Hydrogen bonds: A:D.507, A:N.651, A:T.655, A:Y.729 Water bridges: A:R.648, A:R.648, A:R.648, A:R.648, A:R.662, A:R.662, A:R.662 Salt bridges: A:D.507, A:R.648 A3C.5: 6 residues within 4Å: Chain A: R.474, E.477, V.478, S.481, F.728, Y.729 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.478, A:F.728, A:F.728, A:F.728, A:F.728 Salt bridges: A:R.474

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

EDO.6: 4 residues within 4Å: Chain A: M.308, W.396, Y.703, N.720 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.396, A:N.720, A:N.720 Water bridges: A:S.716 EDO.7: 7 residues within 4Å: Chain A: S.251, N.297, L.301, R.340, N.344, W.418, L.429 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.251, A:N.297, A:N.344 EDO.8: 5 residues within 4Å: Chain A: W.280, E.282, V.313, S.314, V.317 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.280, A:S.314 Water bridges: A:E.282, A:S.314, A:S.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koksal, M. et al., Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis. Nature (2011)

Release Date

2010-12-29

Peptides

Taxadiene synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Taxadiene synthase

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