SMTL ID : 7bur.1

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x NAR: NARINGENIN(Non-covalent)

NAR.1: 18 residues within 4Å: Chain A: S.149, C.180, E.208, I.209, T.210, T.213, F.231, G.232, D.233, I.269, D.270, G.271, L.278, T.279, F.280, N.351, S.353, P.390 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.208, A:T.213, A:F.231, A:F.231, A:F.231, A:I.269, A:L.278, A:F.280 Hydrogen bonds: A:G.232, A:D.270, A:S.353 NAR.4: 18 residues within 4Å: Chain B: T.148, S.149, C.180, E.208, I.209, T.210, T.213, F.231, G.232, D.233, I.269, D.270, G.271, L.278, T.279, F.280, S.353, P.390 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.208, B:T.213, B:F.231, B:F.231, B:F.231, B:F.231, B:I.269, B:L.278, B:F.280 Hydrogen bonds: B:E.208, B:D.233, B:D.270, B:S.353

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 6 residues within 4Å: Chain A: K.83, H.344, E.348, Y.349, Q.363, K.366 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.349 Hydrogen bonds: A:E.348, A:Y.349, A:Y.349, A:K.366, A:K.366 Water bridges: A:Y.349, A:Q.363 Salt bridges: A:K.83, A:K.366, A:K.366 CIT.3: 9 residues within 4Å: Chain A: C.180, F.280, L.282, V.286, P.287, G.320, G.321, A.323, I.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.321, A:A.323, A:I.324 CIT.5: 7 residues within 4Å: Chain A: E.275 Chain B: S.98, P.105, S.106, L.107, D.108, A.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.108, B:A.109 Water bridges: B:S.98 CIT.6: 11 residues within 4Å: Chain B: C.180, V.226, L.230, F.231, I.269, F.280, L.282, V.286, G.320, I.324, N.351 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.320, B:N.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imaizumi, R. et al., Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean. Proteins (2020)

Release Date

2020-08-19

Peptides

Chalcone synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chalcone synthase 1

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