SMTL ID : 8dqp.1

Crystal structure of Arabidopsis thaliana COSY in complex with scopoletin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

1 x T83: 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one(Non-covalent)

T83.1: 10 residues within 4Å: Chain A: F.40, Y.42, I.159, H.161, C.164, D.165, G.166, A.169, W.371 Ligands: PG4.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.40, A:Y.42, A:W.371 Hydrogen bonds: A:Y.42, A:C.164 Salt bridges: A:H.161 pi-Stacking: A:F.40, A:F.40, A:H.161

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: R.211, L.214 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.211, A:L.214 CA.7: 2 residues within 4Å: Chain B: R.211, L.214 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.211, B:L.214, H2O.4

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

EDO.3: 8 residues within 4Å: Chain A: D.31, N.32, D.33, N.34, L.36, H.37, F.89, A.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.34 Water bridges: A:N.32, A:N.87, A:H.355 EDO.4: 5 residues within 4Å: Chain A: S.215, D.217, F.220, N.360, G.362 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.217, A:D.217 Water bridges: A:N.360, A:N.360

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 11 residues within 4Å: Chain A: L.36, H.161, F.260, Y.287, S.288, F.368, T.369, D.370, L.396, L.397 Ligands: T83.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.288, A:S.288, A:D.370, A:L.397

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 7 residues within 4Å: Chain A: Q.225, G.364, V.365, S.399, M.400, E.401, R.429 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.225, A:G.364, A:M.400, A:E.401 Water bridges: A:V.365, A:V.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, C.Y. et al., Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY. Nat Commun (2023)

Release Date

2023-01-11

Peptides

Coumarin Synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coumarin Synthase

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