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

Crystal structure of N299A/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 Compare

Method

X-RAY DIFFRACTION 2.53 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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.213, A:S.217, A:Y.309 Water bridges: A:R.169, A:R.169, A:D.172, A:D.172, A:K.220, A:K.220, A:R.308, A:R.308 Salt bridges: A:R.169, A:K.220, 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 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.213, B:N.213, B:S.217, B:Y.309 Water bridges: B:D.84, B:E.88, B:E.88, B:E.88, B:R.169, B:R.169, B:R.169, B:D.172, B:D.172, B:K.220, B:K.220, B:K.220, B:R.308 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, JF1.16 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:D.84, C:N.213, C:S.217 Water bridges: C:Q.151, C:R.169, C:R.169, C:R.169, C:D.172, C:K.220, C:K.220, C:K.220, C:E.221, C:R.308 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 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.84, D:N.213, D:S.217 Water bridges: D:R.169, D:D.172, D:D.172, D:K.220, D:K.220 Salt bridges: D:R.169, D:K.220, D:K.220, D:R.308

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.84, D.172 Ligands: POP.1, MG.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.84, H2O.2, H2O.2, H2O.2, H2O.3 MG.3: 5 residues within 4Å: Chain A: D.84, E.88, K.220 Ligands: POP.1, MG.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.84, H2O.1, H2O.1, H2O.2 MG.4: 4 residues within 4Å: Chain A: N.213, 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: 3 residues within 4Å: Chain B: D.84 Ligands: POP.6, MG.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.84, H2O.4, H2O.4, H2O.4, H2O.5 MG.8: 5 residues within 4Å: Chain B: D.84, E.88, K.220 Ligands: POP.6, MG.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.84, H2O.4, H2O.4, H2O.5 MG.9: 4 residues within 4Å: Chain B: N.213, S.217, E.221 Ligands: POP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.217, B:E.221, H2O.4 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.6, H2O.6, H2O.6, H2O.7 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.5, H2O.6, H2O.6 MG.14: 4 residues within 4Å: Chain C: N.213, S.217, E.221 Ligands: POP.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.217, C:E.221, H2O.5 MG.18: 3 residues within 4Å: Chain D: D.84 Ligands: POP.17, MG.19 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.84, H2O.10, H2O.10, H2O.11, H2O.11 MG.19: 6 residues within 4Å: Chain D: D.84, E.88, K.220, R.308 Ligands: POP.17, MG.18 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.84, H2O.10, H2O.11 MG.20: 5 residues within 4Å: Chain D: R.169, N.213, S.217, E.221 Ligands: POP.17 4 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:S.217, D:E.221, H2O.10, 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: 10 residues within 4Å: Chain A: Y.61, L.80, F.81, F.147, D.172, V.173, L.178, L.209, N.213 Ligands: POP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.61, A:F.147, A:F.147, A:L.178, A:N.213 Salt bridges: A:D.84 JF1.10: 8 residues within 4Å: Chain B: Y.61, L.80, F.81, F.147, V.173, L.178, N.213 Ligands: POP.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.80, B:F.81, B:F.147, B:F.147, B:V.173, B:L.178 JF1.16: 9 residues within 4Å: Chain C: Y.61, L.80, F.81, F.147, V.173, L.178, L.209, N.213 Ligands: POP.11 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.61, C:F.147, C:V.173, C:L.178, C:N.213 JF1.21: 9 residues within 4Å: Chain D: Y.61, F.81, D.84, F.147, V.173, L.178, L.209, N.213 Ligands: POP.17 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.81, D:F.81, D:F.147, D:L.178, D:L.209, D:N.213

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 7 residues within 4Å: Chain C: R.107, E.142, R.149 Chain D: R.197, E.200, L.275, L.280 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.107, C:R.149, C:R.149, D:E.200 Water bridges: C:R.107

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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