SMTL ID : 7x5r.1

Crystal structure of AtHPPD-Lancotrione complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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: 9P5.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.198, A:H.280, A:E.366, H2O.4 CO.6: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: 9P5.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.198, B:H.280, B:E.366, H2O.14

2 x 9P5: (1R,3R)-2-[(S)-[2-chloranyl-3-[2-(1,3-dioxolan-2-yl)ethoxy]-4-methylsulfonyl-phenyl]-oxidanyl-methyl]cyclohexane-1,3-diol(Non-covalent)

9P5.2: 19 residues within 4Å: Chain A: H.198, V.200, S.239, P.252, N.254, H.280, M.307, L.340, Q.351, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.1, BCN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.252, A:F.353, A:F.364, A:F.391, A:F.396 Water bridges: A:Q.351 9P5.7: 19 residues within 4Å: Chain B: H.198, V.200, S.239, P.252, N.254, H.280, M.307, L.340, Q.351, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.6, BCN.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.252, B:F.353, B:F.364, B:F.391, B:F.396 Water bridges: B:Q.351

2 x BCN: BICINE(Non-covalent)

BCN.3: 8 residues within 4Å: Chain A: M.307, T.354, K.355, P.356, P.361, T.362, F.364 Ligands: 9P5.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.265 BCN.8: 8 residues within 4Å: Chain B: M.307, T.354, K.355, P.356, P.361, T.362, F.364 Ligands: 9P5.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.265

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

MPD.4: 5 residues within 4Å: Chain A: T.30, R.34, F.44, K.47, Y.60 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.34, A:F.44, A:K.47, A:Y.60, A:Y.60 Hydrogen bonds: A:R.34, A:R.34 MPD.5: 6 residues within 4Å: Chain A: S.99, S.102, F.103, S.106, R.112, D.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.102 Water bridges: A:S.99 MPD.9: 5 residues within 4Å: Chain B: T.30, R.34, F.44, K.47, Y.60 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.34, B:F.44, B:K.47, B:Y.60, B:Y.60 Hydrogen bonds: B:R.34, B:R.34 MPD.10: 6 residues within 4Å: Chain B: S.99, S.102, F.103, S.106, R.112, D.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.102 Water bridges: B:S.99

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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