SMTL ID : 7x6m.1

Crystal structure of AtHPPD-Y191058 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: 9ZU.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.198, A:H.280, A:E.366, H2O.2 CO.6: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: 9ZU.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.198, B:H.280, B:E.366, H2O.11

2 x 9ZU: 5-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-phenyl-2-(trifluoromethyl)quinazolin-4-one(Non-covalent)

9ZU.2: 17 residues within 4Å: Chain A: H.198, V.200, S.239, P.252, N.254, H.280, M.307, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.1, MPD.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.252, A:F.353, A:F.353, A:F.364, A:F.391, A:F.396 Water bridges: A:N.254, A:Q.265, A:Q.351 pi-Stacking: A:F.396 Halogen bonds: A:N.395 9ZU.7: 17 residues within 4Å: Chain B: H.198, V.200, S.239, P.252, N.254, H.280, M.307, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.6, MPD.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.252, B:F.353, B:F.353, B:F.364, B:F.391, B:F.396 Water bridges: B:Q.265, B:Q.351 pi-Stacking: B:F.396 Halogen bonds: B:N.395

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 7 residues within 4Å: Chain A: Q.265, M.307, T.354, K.355, P.356, F.364 Ligands: 9ZU.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.265, A:F.364, A:F.364 Water bridges: A:P.361 MPD.4: 8 residues within 4Å: Chain A: V.56, E.83, I.84, K.85, T.88, A.90, P.93, F.95 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.56, A:E.83, A:A.90 Water bridges: A:S.80, A:E.83 MPD.5: 2 residues within 4Å: Chain A: R.298, I.301 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.298, A:I.301 MPD.8: 7 residues within 4Å: Chain B: Q.265, M.307, T.354, K.355, P.356, F.364 Ligands: 9ZU.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.265, B:F.364, B:F.364 Water bridges: B:P.361 MPD.9: 8 residues within 4Å: Chain B: V.56, E.83, I.84, K.85, T.88, A.90, P.93, F.95 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.56, B:E.83, B:A.90 Water bridges: B:S.80, B:E.83 MPD.10: 2 residues within 4Å: Chain B: R.298, I.301 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.298, B:I.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules. Adv Agrochem (2022)

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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