SMTL ID : 5t95.1

Prephenate Dehydrogenase M219T, N222D mutant from Soybean

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: G.16, F.17, G.18, N.19, F.20, S.39, R.40, S.41, Y.43, C.72, T.73, S.74, I.75, S.77, E.80, V.81, V.99, L.100, S.101, H.124, P.125, F.127, G.128, P.129, D.222, S.223, L.226 Ligands: TYR.2 33 PLIP interactions: 29 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:G.16, A:G.18, A:N.19, A:F.20, A:S.39, A:S.39, A:R.40, A:S.41, A:Y.43, A:T.73, A:S.74, A:S.74, A:I.75, A:S.77, A:E.80, A:S.101, A:F.127, A:S.223 Water bridges: A:G.21, A:R.40, A:R.40, A:S.41, A:Y.43, A:S.223, A:S.223, Y.2, Y.2 Salt bridges: A:R.40 pi-Stacking: A:F.20 pi-Cation interactions: A:R.40, A:R.40 Hydrophobic interactions: Y.2, Y.2 NAP.3: 28 residues within 4Å: Chain B: G.16, F.17, G.18, N.19, F.20, S.39, R.40, S.41, Y.43, C.72, T.73, S.74, I.75, S.77, E.80, V.81, V.99, L.100, S.101, H.124, P.125, F.127, G.128, P.129, D.222, S.223, L.226 Ligands: TYR.4 33 PLIP interactions: 29 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: B:G.16, B:G.18, B:N.19, B:F.20, B:S.39, B:S.39, B:R.40, B:S.41, B:T.73, B:T.73, B:S.74, B:S.74, B:I.75, B:S.77, B:E.80, B:S.101, B:F.127, B:S.223 Water bridges: B:N.19, B:G.21, B:R.40, B:R.40, B:S.41, B:D.222, B:D.222, Y.4, Y.4 Salt bridges: B:R.40 pi-Stacking: B:F.20 pi-Cation interactions: B:R.40, B:R.40 Hydrophobic interactions: Y.4, Y.4

2 x TYR: TYROSINE(Non-covalent)

TYR.2: 10 residues within 4Å: Chain A: S.101, H.124, F.127, G.128, P.129, Q.130, T.131, Q.184, D.222 Ligands: NAP.1 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:H.124, A:G.128, A:Q.130, A:Q.130, A:T.131, A:Q.184, A:D.222, Y.2 Water bridges: A:Q.130, A:D.222 TYR.4: 12 residues within 4Å: Chain B: S.101, H.124, F.127, G.128, P.129, Q.130, T.131, Q.184, H.188, D.222, L.226 Ligands: NAP.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.226 Hydrogen bonds: B:S.101, B:G.128, B:Q.130, B:T.131, B:Q.184, B:D.222 Water bridges: B:M.126, B:Q.130, B:T.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schenck, C.A. et al., Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants. Nat. Chem. Biol. (2017)

Release Date

2017-06-28

Peptides

Prephenate dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prephenate dehydrogenase 1