SMTL ID : 5imi.3 (2 other biounits)

Crystal structure of S303A Aspergillus terreus aristolochene synthase complexed with (1S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)decahydroquinolizin-5-ium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

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

POP.1: 13 residues within 4Å: Chain A: F.81, D.84, R.169, N.213, S.217, K.220, E.221, R.308, Y.309 Ligands: MG.2, MG.3, MG.4, JF1.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.213, A:S.217, A:E.221, A:Y.309 Water bridges: A:R.169, A:R.169, A:R.169, A:K.220, A:K.220, A:R.308 Salt bridges: A:R.169, A:K.220, A:R.308 POP.6: 13 residues within 4Å: Chain B: F.81, D.84, R.169, N.213, S.217, K.220, E.221, R.308, Y.309 Ligands: MG.7, MG.8, MG.9, JF1.10 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.84, B:N.213, B:S.217, B:S.217, B:Y.309 Water bridges: B:R.169, B:R.169, B:K.220 Salt bridges: B:R.169, B:K.220, B:R.308 POP.11: 13 residues within 4Å: Chain C: F.81, D.84, R.169, N.213, S.217, K.220, E.221, R.308, Y.309 Ligands: MG.12, MG.13, MG.14, JF1.15 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:D.84, C:N.213, C:S.217, C:Y.309 Water bridges: C:D.84, C:D.84, C:D.84, C:R.169, C:R.169, C:D.172, C:D.172, C:D.214, C:K.220, C:K.220, C:K.220 Salt bridges: C:R.169, C:K.220, C:R.308 POP.17: 13 residues within 4Å: Chain D: F.81, D.84, R.169, N.213, S.217, K.220, E.221, R.308, Y.309 Ligands: MG.18, MG.19, MG.20, JF1.21 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.213, D:S.217 Water bridges: D:R.169, D:R.169, D:D.172, D:D.172 Salt bridges: D:R.169, D:K.220, D:K.220, D:R.308

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.84 Ligands: POP.1, MG.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.84, H2O.4, H2O.4, H2O.6 MG.3: 5 residues within 4Å: Chain A: D.84, E.88, K.220 Ligands: POP.1, MG.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, H2O.1, H2O.4 MG.4: 5 residues within 4Å: Chain A: N.213, D.214, S.217, E.221 Ligands: POP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.217, A:E.221, H2O.2 MG.7: 4 residues within 4Å: Chain B: D.84, D.172 Ligands: POP.6, MG.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, H2O.8, H2O.9 MG.8: 6 residues within 4Å: Chain B: D.84, E.88, K.220, E.221 Ligands: POP.6, MG.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, H2O.8, H2O.9 MG.9: 4 residues within 4Å: Chain B: N.213, S.217, E.221 Ligands: POP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.217, B:E.221 MG.12: 3 residues within 4Å: Chain C: D.84 Ligands: POP.11, MG.13 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.84, H2O.11, H2O.13, H2O.15, H2O.17 MG.13: 4 residues within 4Å: Chain C: D.84, E.88 Ligands: POP.11, MG.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.84, H2O.11, H2O.13, H2O.17 MG.14: 4 residues within 4Å: Chain C: N.213, S.217, E.221 Ligands: POP.11 4 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:S.217, C:E.221, H2O.10, POP.11 MG.18: 4 residues within 4Å: Chain D: D.84, D.172 Ligands: POP.17, MG.19 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.84, H2O.21, H2O.22, H2O.22, H2O.23 MG.19: 5 residues within 4Å: Chain D: D.84, E.88, K.220 Ligands: POP.17, MG.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.84, D:E.88, H2O.22 MG.20: 5 residues within 4Å: Chain D: R.169, N.213, S.217, E.221 Ligands: POP.17 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:S.217, D:E.221, POP.17

4 x JF1: (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium(Non-covalent)

JF1.5: 11 residues within 4Å: Chain A: V.57, Y.61, F.81, F.147, D.172, V.173, L.177, N.213, N.299, W.302 Ligands: POP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.57, A:Y.61, A:F.81, A:F.81, A:F.147, A:L.177, A:W.302 JF1.10: 10 residues within 4Å: Chain B: V.57, Y.61, F.81, F.147, V.173, L.177, N.213, N.299, W.302 Ligands: POP.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.57, B:Y.61, B:Y.61, B:F.81, B:F.81, B:F.81, B:F.147, B:L.177, B:W.302 JF1.15: 13 residues within 4Å: Chain C: V.57, Y.61, L.77, L.80, F.81, D.84, F.147, D.172, V.173, N.213, N.299, W.302 Ligands: POP.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.57, C:Y.61, C:L.77, C:F.81, C:F.81, C:D.84, C:F.147, C:W.302 JF1.21: 11 residues within 4Å: Chain D: V.57, Y.61, F.81, D.84, F.147, D.172, V.173, N.213, N.299, W.302 Ligands: POP.17 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.57, D:Y.61, D:F.81, D:F.81, D:D.84, D:F.147, D:W.302

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 7 residues within 4Å: Chain C: R.107, E.142, R.149 Chain D: R.197, E.200, L.275, L.280 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.107, C:R.149, C:R.149, D:E.200 Water bridges: C:R.107, D:E.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, M. et al., Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase. Biochemistry (2016)

Release Date

2016-05-25

Peptides

Aristolochene synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

Aristolochene synthase

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