SMTL ID : 1yyu.1

D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4S)-7-azabisabolene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.225, D.226, S.229, E.233 Ligands: POP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.229, A:E.233 MG.2: 3 residues within 4Å: Chain A: E.233, D.239 Ligands: POP.4 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: E.100 Ligands: POP.9 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: N.225, D.226, S.229, E.233 Ligands: POP.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.229, B:E.233

1 x RAZ: (1R)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM(Non-covalent)

RAZ.3: 13 residues within 4Å: Chain A: I.70, M.73, Y.93, T.96, L.97, R.182, G.186, L.187, N.225, Y.295, W.298, Y.305 Ligands: POP.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.93, A:L.97, A:L.187, A:W.298

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 10 residues within 4Å: Chain A: R.182, N.225, S.229, K.232, E.233, R.304, Y.305 Ligands: MG.1, MG.2, RAZ.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.225, A:S.229, A:E.233, A:Y.305 Water bridges: A:R.304, A:R.304 Salt bridges: A:R.182, A:K.232, A:R.304 POP.9: 10 residues within 4Å: Chain B: R.182, N.225, S.229, K.232, E.233, R.304, Y.305 Ligands: MG.6, MG.7, SAZ.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.225, B:N.225, B:S.229, B:Y.305 Water bridges: B:E.100, B:K.232 Salt bridges: B:R.182, B:K.232, B:R.304

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

EDO.5: 5 residues within 4Å: Chain A: Y.113, W.128, N.132, F.135 Chain B: F.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.113, A:N.132 EDO.10: 7 residues within 4Å: Chain A: F.114 Chain B: Y.113, L.117, W.128, N.132, F.135, I.151 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.113, B:Y.113, B:N.132

1 x SAZ: (1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM(Non-covalent)

SAZ.8: 14 residues within 4Å: Chain B: I.70, M.73, Y.93, T.96, L.97, R.182, N.185, G.186, L.187, M.221, N.225, Y.295, W.298 Ligands: POP.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.70, B:L.97, B:L.187, B:W.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vedula, L.S. et al., Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants. Biochemistry (2005)

Release Date

2005-03-29

Peptides

Trichodiene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trichodiene synthase

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