SMTL ID : 7xnt.1

Crystal structure of PfHPPD-Y13161 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

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

CO.1: 4 residues within 4Å: Chain A: H.161, H.240, E.322 Ligands: 94L.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.161, A:H.240, A:E.322, H2O.1 CO.3: 4 residues within 4Å: Chain B: H.161, H.240, E.322 Ligands: 94L.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.161, B:H.240, B:E.322, H2O.7 CO.5: 4 residues within 4Å: Chain C: H.161, H.240, E.322 Ligands: 94L.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.161, C:H.240, C:E.322, H2O.13 CO.7: 4 residues within 4Å: Chain D: H.161, H.240, E.322 Ligands: 94L.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.161, D:H.240, D:E.322, H2O.14

4 x 94L: 3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione(Non-covalent)

94L.2: 20 residues within 4Å: Chain A: H.161, L.199, S.201, P.214, N.216, Q.225, H.240, M.263, L.294, Q.309, F.311, F.320, E.322, F.332, G.333, E.334, N.336, F.337, L.340 Ligands: CO.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.199, A:P.214, A:F.311, A:F.311, A:F.337, A:F.337, A:F.337 Hydrogen bonds: A:Q.225 Water bridges: A:Q.239, A:Q.309 94L.4: 17 residues within 4Å: Chain B: H.161, T.163, S.201, P.214, N.216, Q.225, H.240, F.311, F.320, E.322, F.332, G.333, E.334, N.336, F.337, L.340 Ligands: CO.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.163, B:P.214, B:F.311, B:F.311, B:F.320, B:F.332, B:F.337, B:F.337, B:F.337 Hydrogen bonds: B:Q.225 Water bridges: B:Q.309 94L.6: 19 residues within 4Å: Chain C: H.161, T.163, S.201, P.214, N.216, Q.225, H.240, M.263, Q.309, F.311, F.320, E.322, F.332, G.333, E.334, N.336, F.337, L.340 Ligands: CO.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:P.214, C:F.311, C:F.311, C:F.311, C:F.320, C:F.332, C:E.334, C:F.337, C:F.337 Hydrogen bonds: C:Q.225 Water bridges: C:Q.309 pi-Stacking: C:F.337 94L.8: 16 residues within 4Å: Chain D: H.161, T.163, S.201, P.214, Q.225, H.240, M.263, F.311, F.320, E.322, F.332, G.333, N.336, F.337, L.340 Ligands: CO.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:T.163, D:P.214, D:F.311, D:F.311, D:F.332, D:F.337, D:F.337 Hydrogen bonds: D:Q.225 Water bridges: D:Q.309 pi-Stacking: D:F.337

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

2022-12-14

Peptides

4-hydroxyphenylpyruvate dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

C
B

D
C

4-hydroxyphenylpyruvate dioxygenase

Related Entries With Identical Sequence