SMTL ID : 7ofl.1

Crystal structure of the sesquiterpene synthase Copu9 from coniophora puteana in complex with alendronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x AHD: 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE(Non-covalent)

AHD.1: 15 residues within 4Å: Chain A: F.124, D.127, R.217, T.220, S.221, N.263, S.267, K.270, E.271, R.351, Y.352 Ligands: MG.2, MG.3, MG.4, EDO.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.124 Hydrogen bonds: A:R.217, A:R.217, A:S.221, A:N.263, A:S.267, A:K.270, A:E.271, A:R.351, A:Y.352, A:Y.352 Water bridges: A:E.271 AHD.16: 14 residues within 4Å: Chain B: F.124, D.127, R.217, T.220, S.221, N.263, S.267, K.270, E.271, R.351, Y.352 Ligands: MG.17, MG.18, MG.19 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.124 Hydrogen bonds: B:D.127, B:R.217, B:R.217, B:T.220, B:S.221, B:N.263, B:S.267, B:K.270, B:E.271, B:R.351 Water bridges: B:Q.198, B:Y.352, B:Y.352

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.127, K.270, R.351 Ligands: AHD.1, MG.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.127, H2O.3, H2O.5, H2O.5 MG.3: 5 residues within 4Å: Chain A: R.217, N.263, S.267, E.271 Ligands: AHD.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.267, A:E.271, H2O.4 MG.4: 3 residues within 4Å: Chain A: D.127 Ligands: AHD.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.127, H2O.2, H2O.5, H2O.5, H2O.9 MG.17: 4 residues within 4Å: Chain B: D.127, K.270 Ligands: AHD.16, MG.18 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.127, H2O.17, H2O.17, H2O.17 MG.18: 3 residues within 4Å: Chain B: D.127 Ligands: AHD.16, MG.17 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.127, H2O.17, H2O.17, H2O.20, H2O.22 MG.19: 5 residues within 4Å: Chain B: R.217, N.263, S.267, E.271 Ligands: AHD.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.267, B:E.271, H2O.17

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

EDO.5: 7 residues within 4Å: Chain A: D.56, C.57, T.58, Y.59, I.307, E.311 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.56, A:T.58 Water bridges: A:T.58, A:T.58 EDO.6: 4 residues within 4Å: Chain A: A.249, A.250, E.253, R.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.309 EDO.7: 6 residues within 4Å: Chain A: H.186, D.189, L.190, I.193 Chain B: Y.244 Ligands: EDO.22 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.189 Water bridges: B:H.186 EDO.8: 2 residues within 4Å: Chain A: E.311 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.9: 6 residues within 4Å: Chain A: F.353, D.356, V.360, I.365, V.366, K.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.353, A:I.365, A:K.367 EDO.10: 3 residues within 4Å: Chain A: D.136, W.139 Chain B: H.241 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.241 EDO.11: 4 residues within 4Å: Chain A: C.223, V.259, W.338 Ligands: AHD.1 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.263, A:S.342, A:S.346, A:S.346 EDO.12: 4 residues within 4Å: Chain A: A.194, Q.197, T.215, V.216 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.194 EDO.13: 4 residues within 4Å: Chain A: L.63, D.65, P.106, H.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.65, A:H.107 Water bridges: A:D.65 EDO.14: 3 residues within 4Å: Chain A: W.77, R.114, R.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.114, A:R.114 EDO.15: 4 residues within 4Å: Chain A: S.111, R.114, V.115, R.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.111, A:R.171 EDO.20: 5 residues within 4Å: Chain A: H.186, Y.244 Chain B: H.186, L.190, I.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.186 Water bridges: B:D.189, B:D.189 EDO.21: 4 residues within 4Å: Chain B: Y.59, E.311, R.314, Q.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.311, B:Q.336 EDO.22: 6 residues within 4Å: Chain B: E.182, R.183, H.186, T.187, Y.244 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.182, B:Y.244 Water bridges: B:R.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ringel, M. et al., Biotechnological potential and initial characterization of two novel sesquiterpene synthases from Basidiomycota Coniophora puteana for heterologous production of delta-cadinol. Microb Cell Fact (2022)

Release Date

2022-03-16

Peptides

Terpene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Terpene synthase