SMTL ID : 5xgk.1 (1 other biounit)

Crystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (AtHPPD) complexed with its substrate 4-hydroxyphenylpyruvate acid (HPPA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

1 x TYF: (2S)-2-hydroxy-3-(4-hydroxyphenyl)propanoic acid(Non-covalent)

TYF.1: 11 residues within 4Å: Chain A: H.226, V.228, S.267, H.308, Q.379, F.381, E.394, F.419, G.420, N.423 Ligands: FE.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.267, A:Q.379, A:N.423 Salt bridges: A:H.226, A:H.308 pi-Stacking: A:F.381

2 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: H.226, V.228, H.308, E.394 Ligands: TYF.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.226, A:H.308, A:E.394, H2O.1 FE.5: 3 residues within 4Å: Chain B: H.226, H.308, E.394 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.226, B:H.308, B:E.394

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

ACT.3: 5 residues within 4Å: Chain A: H.300, R.388 Chain B: Y.103, S.104, L.107 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.107, A:H.300 Hydrogen bonds: B:S.104 Salt bridges: A:H.300, A:R.388 ACT.4: 4 residues within 4Å: Chain A: A.61, R.62, F.72, Y.88 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.61, A:F.72, A:Y.88 Salt bridges: A:R.62 ACT.6: 4 residues within 4Å: Chain B: A.61, R.62, F.72, Y.88 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.61, B:F.72, B:Y.88 Salt bridges: B:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, H.Y. et al., Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery. Res (2019)

Release Date

2018-09-19

Peptides

4-hydroxyphenylpyruvate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-hydroxyphenylpyruvate dioxygenase

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