SMTL ID : 2q5o.2 (1 other biounit)

X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.449, N.476, S.478, E.480 Ligands: TPW.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.449, A:S.478, H2O.11 MG.5: 4 residues within 4Å: Chain B: D.449, N.476, S.478 Ligands: TPW.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.449, B:S.478, H2O.25

2 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TPW.2: 23 residues within 4Å: Chain A: G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482 Chain B: P.43, G.44, E.68, A.94, H.133 Ligands: MG.1, PPY.7 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.479, A:W.479, A:L.482 Hydrogen bonds: A:M.400, A:D.402, A:A.422, A:M.424, A:G.450, A:A.451, A:N.476, A:E.480, A:M.481 Water bridges: A:C.403, A:G.448, A:G.448, A:D.449, A:N.476 TPW.6: 24 residues within 4Å: Chain A: I.42, P.43, G.44, E.68, A.94, H.133 Chain B: G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, M.454, N.476, S.478, W.479, E.480, M.481, L.482 Ligands: PPY.3, MG.5 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.479, B:W.479, B:L.482, B:L.482, B:L.482, A:A.94 Hydrogen bonds: B:D.402, B:A.422, B:M.424, B:G.450, B:A.451, B:N.476, B:E.480, B:M.481 Water bridges: B:C.403, B:D.449, B:N.476

4 x PPY: 3-PHENYLPYRUVIC ACID(Non-covalent)

PPY.3: 12 residues within 4Å: Chain A: G.44, D.45, H.132, H.133 Chain B: T.303, A.422, M.481, L.482, F.485, F.552, Q.556 Ligands: TPW.6 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.45, A:D.45 Water bridges: A:F.46 Salt bridges: A:H.133 pi-Stacking: A:H.132 Hydrophobic interactions: B:T.303, B:A.422, B:F.485, B:F.552, B:Q.556 PPY.4: 12 residues within 4Å: Chain A: R.80, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.262, A:L.395 Hydrogen bonds: A:A.417 Salt bridges: A:R.80, A:R.235 PPY.7: 12 residues within 4Å: Chain A: T.303, A.422, M.481, L.482, F.485, F.552, Q.556 Chain B: G.44, D.45, H.132, H.133 Ligands: TPW.2 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.303, A:F.485, A:F.552 Hydrogen bonds: B:D.45, B:D.45 Water bridges: B:F.46 Salt bridges: B:H.133 pi-Stacking: B:H.132 PPY.8: 11 residues within 4Å: Chain B: R.80, R.234, R.235, M.258, R.260, G.261, L.262, G.414, L.415, M.416, A.417 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.417 Salt bridges: B:R.80, B:R.235

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain B: V.544, L.545, D.547 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.545 Water bridges: B:D.547, B:D.547

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Versees, W. et al., Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase. J.Biol.Chem. (2007)

Release Date

2007-10-23

Peptides

Phenylpyruvate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phenylpyruvate decarboxylase

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