SMTL ID : 7x8i.1

Crystal structure of AtHPPD-Shikonin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: H.198, H.280, E.366 Ligands: FNO.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.198, A:H.280, A:E.366 CO.3: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: FNO.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.198, B:H.280, B:E.366

2 x FNO: 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione(Non-covalent)

FNO.2: 13 residues within 4Å: Chain A: H.198, L.237, S.239, Q.265, Q.279, H.280, M.307, F.353, F.364, E.366, F.391, F.396 Ligands: CO.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.353, A:F.364, A:F.391 Hydrogen bonds: A:S.239, A:Q.265, A:Q.279 FNO.4: 13 residues within 4Å: Chain B: H.198, L.237, S.239, Q.265, Q.279, H.280, M.307, F.353, F.364, E.366, F.391, F.396 Ligands: CO.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.353, B:F.364, B:F.391 Hydrogen bonds: B:S.239, B:Q.265, B:Q.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Discovery of Subnanomolar Inhibitors of 4-Hydroxyphenylpyruvate Dioxygenase via Structure-Based Rational Design. J.Agric.Food Chem. (2023)

Release Date

2022-06-01

Peptides

4-hydroxyphenylpyruvate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxyphenylpyruvate dioxygenase

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