SMTL ID : 8hxg.1

Crystal structure of AtHPPD-Y14116 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: NUL.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.4: 4 residues within 4Å: Chain B: H.198, H.280, E.366 Ligands: NUL.5 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 NUL: (1S,2R,3R)-2-[(S)-(2-methoxy-8-methyl-quinolin-3-yl)-oxidanyl-methyl]-6,6-dimethyl-cyclohex-4-ene-1,3-diol(Non-covalent)

NUL.2: 20 residues within 4Å: Chain A: H.198, V.200, E.224, S.239, V.241, P.252, N.254, H.280, L.340, Q.351, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.1, MPD.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.200, A:V.241, A:L.340, A:F.353, A:F.353, A:F.391, A:F.391, A:N.395, A:L.399 Water bridges: A:Q.279, A:Q.279, A:Q.351 pi-Stacking: A:F.396 NUL.5: 20 residues within 4Å: Chain B: H.198, V.200, E.224, S.239, V.241, P.252, N.254, H.280, L.340, Q.351, F.353, F.364, E.366, F.391, G.392, N.395, F.396, L.399 Ligands: CO.4, MPD.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.200, B:V.241, B:L.340, B:F.353, B:F.353, B:F.391, B:F.391, B:N.395, B:L.399 Water bridges: B:Q.279, B:Q.279, B:Q.351 pi-Stacking: B:F.396

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

MPD.3: 7 residues within 4Å: Chain A: M.307, F.353, T.354, K.355, P.356, F.364 Ligands: NUL.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.353, A:F.364, A:F.364 Hydrogen bonds: A:T.354 MPD.6: 7 residues within 4Å: Chain B: M.307, F.353, T.354, K.355, P.356, F.364 Ligands: NUL.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.353, B:F.364, B:F.364 Hydrogen bonds: B:T.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Crystal structure of AtHPPD-Y14116 complex. To Be Published

Release Date

2023-12-20

Peptides

4-hydroxyphenylpyruvate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-hydroxyphenylpyruvate dioxygenase

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