SMTL ID : 7x5y.1

Crystal structure of AtHPPD-Y14240 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: HZS.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.5: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: HZS.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.198, B:H.280, B:E.366, H2O.12

2 x HZS: (1R,3S)-5-methyl-2-[(1S)-2-naphthalen-1-yloxy-1-oxidanyl-ethyl]cyclohexane-1,3-diol(Non-covalent)

HZS.2: 18 residues within 4Å: Chain A: H.198, V.200, E.224, S.239, P.252, N.254, H.280, L.340, Q.351, I.352, F.353, E.366, F.391, G.392, N.395, F.396 Ligands: CO.1, MPD.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.252, A:L.340, A:L.340, A:Q.351, A:N.395 Hydrogen bonds: A:Q.351 pi-Stacking: A:F.353, A:F.396 HZS.6: 18 residues within 4Å: Chain B: H.198, V.200, E.224, S.239, P.252, N.254, H.280, L.340, Q.351, I.352, F.353, E.366, F.391, G.392, N.395, F.396 Ligands: CO.5, MPD.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.252, B:L.340, B:L.340, B:Q.351, B:N.395 Hydrogen bonds: B:Q.351 pi-Stacking: B:F.353, B:F.396

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

MPD.3: 9 residues within 4Å: Chain A: V.56, S.80, E.83, I.84, K.85, T.88, A.90, P.93, F.95 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.83, A:A.90 Hydrogen bonds: A:E.83, A:E.83, A:T.88 Water bridges: A:F.95, A:H.97 MPD.4: 8 residues within 4Å: Chain A: L.237, Q.265, I.266, Q.279, H.280, F.353, F.396 Ligands: HZS.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.237, A:Q.265, A:F.353, A:F.353, A:F.396 Hydrogen bonds: A:Q.279, A:Q.279 MPD.7: 9 residues within 4Å: Chain B: V.56, S.80, 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:E.83, B:A.90 Hydrogen bonds: B:E.83 Water bridges: B:F.95, B:D.96 MPD.8: 8 residues within 4Å: Chain B: L.237, Q.265, I.266, Q.279, H.280, F.353, F.396 Ligands: HZS.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.237, B:Q.265, B:F.353, B:F.353, B:F.396 Hydrogen bonds: B:Q.279, 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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