SMTL ID : 2q5l.2 (1 other biounit)

X-ray structure of phenylpyruvate decarboxylase in complex with 2-(1-hydroxyethyl)-3-deaza-ThDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 Ligands: S1T.3, R1T.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.449, A:S.478, H2O.4 MG.6: 5 residues within 4Å: Chain B: D.449, N.476, S.478 Ligands: S1T.8, R1T.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.449, B:S.478, H2O.32

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: C.230, V.231, T.256, A.298, I.299, Y.420 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain B: C.230, V.231, T.256, M.258, A.298, I.299, Y.420 Ligand excluded by PLIP

2 x S1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1S)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

S1T.3: 24 residues within 4Å: Chain A: M.400, G.401, D.402, A.422, G.423, M.424, G.448, D.449, G.450, A.451, N.476, S.478, W.479, E.480, M.481, L.482 Chain B: P.43, G.44, D.45, E.68, T.91, A.94 Ligands: MG.1, R1T.4 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.479, A:L.482, B:D.45, B:A.94 Hydrogen bonds: 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:D.449, A:D.449, B:D.45, B:G.95 S1T.8: 25 residues within 4Å: Chain A: P.43, G.44, D.45, E.68, T.91, G.95 Chain B: M.400, 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: MG.6, R1T.9 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.479, B:L.482, B:L.482, A:D.45 Hydrogen bonds: B:D.402, B:A.422, B:A.422, B:M.424, B:G.448, 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, A:E.68

2 x R1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

R1T.4: 22 residues within 4Å: Chain A: M.400, 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 Ligands: MG.1, S1T.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.479, A:L.482, A:L.482, A:L.482 Hydrogen bonds: 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:D.449, A:D.449, B:D.45, B:G.95 R1T.9: 24 residues within 4Å: Chain A: P.43, G.44, D.45, E.68, T.91, G.95 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: MG.6, S1T.8 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:M.424, B:W.479, B:L.482, B:L.482, A:T.91 Hydrogen bonds: B:D.402, B:A.422, 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, A:D.45

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: S.83, T.84, P.112, R.173, S.176, R.235, Y.236 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.176 Water bridges: A:S.83, A:T.84, A:L.85, A:Y.236 GOL.10: 7 residues within 4Å: Chain B: S.83, T.84, P.112, R.173, S.176, R.235, Y.236 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.83, B:S.176

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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