SMTL ID : 2q5j.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.449, G.450, F.474, N.476, S.478 Ligands: TPW.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.449, A:S.478 MG.3: 5 residues within 4Å: Chain B: D.449, F.474, N.476, S.478 Ligands: TPW.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.449, B:S.478 MG.5: 6 residues within 4Å: Chain C: D.449, G.450, F.474, N.476, S.478 Ligands: TPW.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.449, C:S.478 MG.7: 5 residues within 4Å: Chain D: D.449, F.474, N.476, S.478 Ligands: TPW.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.449, D:S.478

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

TPW.2: 21 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, E.68, A.94 Ligands: MG.1 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.479, A:L.482, A:L.482, A:L.482, B:A.94 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:D.402 TPW.4: 20 residues within 4Å: Chain A: I.42, P.43, G.44, E.68 Chain B: M.400, D.402, A.422, 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.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:M.424, B:W.479, B:W.479, B:L.482 Hydrogen bonds: B:M.400, 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 TPW.6: 21 residues within 4Å: Chain C: 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 D: P.43, G.44, E.68, A.94 Ligands: MG.5 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.479, C:L.482, C:L.482, C:L.482, D:A.94 Hydrogen bonds: C:M.400, C:D.402, C:A.422, C:M.424, C:G.450, C:A.451, C:E.480, C:M.481 Water bridges: C:N.476 TPW.8: 20 residues within 4Å: Chain C: I.42, P.43, G.44, E.68 Chain D: M.400, D.402, A.422, 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.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:M.424, D:W.479, D:W.479, D:L.482 Hydrogen bonds: D:M.400, D:D.402, D:A.422, D:M.424, D:G.450, D:A.451, D:N.476, D:E.480, D:M.481 Water bridges: D:C.403

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Phenylpyruvate decarboxylase

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