SMTL ID : 2q5q.1 (1 other biounit)

X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and 5-phenyl-2-oxo-valeric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.449, N.476, S.478 Ligands: TPW.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.449, A:S.478, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.449, N.476, S.478 Ligands: TPW.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.449, B:S.478, H2O.21 MG.12: 4 residues within 4Å: Chain C: D.449, N.476, S.478 Ligands: TPW.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.449, C:S.478, H2O.44 MG.18: 4 residues within 4Å: Chain D: D.449, N.476, S.478 Ligands: TPW.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.449, D:S.478, H2O.64

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

TPW.2: 24 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: I.42, P.43, G.44, E.68, A.94, H.133 Ligands: MG.1, KPV.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.479, 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:M.400, A:C.403, A:G.448, A:D.449, A:N.476 TPW.8: 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: KPV.3, MG.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.479, B:L.482 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:D.449 TPW.13: 24 residues within 4Å: Chain C: 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 D: I.42, P.43, G.44, E.68, A.94, H.133 Ligands: MG.12, KPV.20 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:W.479, C:L.482 Hydrogen bonds: C:D.402, C:A.422, C:M.424, C:G.450, C:A.451, C:N.476, C:E.480, C:M.481 Water bridges: C:M.400, C:C.403, C:G.448, C:D.449, C:N.476 TPW.19: 24 residues within 4Å: Chain C: I.42, P.43, G.44, E.68, A.94, H.133 Chain D: 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: KPV.14, MG.18 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.479, D:L.482 Hydrogen bonds: 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, D:D.449, D:D.449, C:E.68

8 x KPV: 5-PHENYL-2-KETO-VALERIC ACID(Non-covalent)

KPV.3: 13 residues within 4Å: Chain A: G.44, D.45, H.132, H.133 Chain B: D.302, T.303, A.422, M.481, L.482, F.485, F.552, Q.556 Ligands: TPW.8 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.485, B:F.552, B:Q.556 pi-Stacking: B:F.552, A:H.132 Hydrogen bonds: A:D.45, A:D.45 Water bridges: A:F.46 Salt bridges: A:H.133 KPV.4: 13 residues within 4Å: Chain A: R.80, Y.81, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.262, A:L.395 Hydrogen bonds: A:A.417 Water bridges: A:G.419 Salt bridges: A:R.80, A:R.235 pi-Cation interactions: A:R.234 KPV.9: 12 residues within 4Å: Chain A: D.302, T.303, A.422, M.481, L.482, F.485, F.552 Chain B: G.44, D.45, H.132, H.133 Ligands: TPW.2 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.303, A:F.485 pi-Stacking: A:F.552, B:H.132 Hydrogen bonds: B:D.45 Water bridges: B:F.46 Salt bridges: B:H.133 KPV.10: 12 residues within 4Å: Chain B: R.80, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.262, B:L.262, B:L.395 Hydrogen bonds: B:A.417 Water bridges: B:G.419 Salt bridges: B:R.80, B:R.235 pi-Cation interactions: B:R.234 KPV.14: 13 residues within 4Å: Chain C: G.44, D.45, H.132, H.133 Chain D: D.302, T.303, A.422, M.481, L.482, F.485, F.552, Q.556 Ligands: TPW.19 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:D.45 Water bridges: C:F.46 Salt bridges: C:H.133 pi-Stacking: C:H.132, D:F.552 Hydrophobic interactions: D:F.485, D:F.552, D:Q.556 KPV.15: 13 residues within 4Å: Chain C: R.80, Y.81, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.262, C:L.395 Hydrogen bonds: C:A.417 Water bridges: C:G.419 Salt bridges: C:R.80, C:R.235 pi-Cation interactions: C:R.234 KPV.20: 12 residues within 4Å: Chain C: D.302, T.303, A.422, M.481, L.482, F.485, F.552 Chain D: G.44, D.45, H.132, H.133 Ligands: TPW.13 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:T.303, C:F.485 pi-Stacking: C:F.552, D:H.132 Hydrogen bonds: D:D.45 Water bridges: D:F.46 Salt bridges: D:H.133 KPV.21: 12 residues within 4Å: Chain D: R.80, R.234, R.235, M.258, R.260, G.261, L.262, L.395, G.414, L.415, M.416, A.417 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.262, D:L.262, D:L.395 Hydrogen bonds: D:A.417 Water bridges: D:G.419 Salt bridges: D:R.80, D:R.235 pi-Cation interactions: D:R.234

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.5: 5 residues within 4Å: Chain A: D.493, L.494, R.542 Chain B: R.463, R.464 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.463, B:R.464, B:R.464, A:D.493, A:D.493 Salt bridges: B:R.464, A:R.542 Water bridges: A:D.493, A:R.542 TLA.16: 5 residues within 4Å: Chain C: D.493, L.494, R.542 Chain D: R.463, R.464 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.463, D:R.464, D:R.464, C:D.493 Salt bridges: D:R.464, C:R.542 Water bridges: C:D.493, C:R.542

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: T.255, G.259, R.260, G.261, L.262, A.264, D.412 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.259, A:R.260, A:G.261, A:L.262, A:D.412 Water bridges: A:R.260, A:Y.363, A:Y.363 GOL.11: 6 residues within 4Å: Chain B: T.255, R.260, G.261, L.262, A.264, D.412 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.259, B:R.260, B:G.261, B:D.412 Water bridges: B:D.412 GOL.17: 7 residues within 4Å: Chain C: T.255, G.259, R.260, G.261, L.262, A.264, D.412 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.259, C:R.260, C:G.261, C:L.262, C:D.412 Water bridges: C:R.260, C:D.412 GOL.22: 6 residues within 4Å: Chain D: T.255, R.260, G.261, L.262, A.264, D.412 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.259, D:R.260, D:G.261, D:D.412 Water bridges: D:Y.363, D:D.412

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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