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

Crystal structure of phenylpyruvate decarboxylase of Azospirillum brasilense

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.449, A:S.478, H2O.1 MG.5: 4 residues within 4Å: Chain B: D.449, N.476, S.478 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.449, B:S.478, H2O.27 MG.10: 4 residues within 4Å: Chain C: D.449, N.476, S.478 Ligands: TPP.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.449, C:S.478, H2O.52 MG.14: 4 residues within 4Å: Chain D: D.449, N.476, S.478 Ligands: TPP.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.449, D:S.478, H2O.79

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

CL.2: 7 residues within 4Å: Chain A: C.230, V.231, T.256, M.258, A.298, I.299, Y.420 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain B: C.230, V.231, T.256, A.298, I.299, Y.420 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain C: C.230, V.231, T.256, M.258, A.298, I.299, Y.420 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain D: C.230, V.231, T.256, A.298, I.299, Y.420 Ligand excluded by PLIP

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 21 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, G.95 Ligands: MG.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B 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:C.403, A:G.448, A:D.449, A:D.449, A:N.476, B:G.95 TPP.7: 21 residues within 4Å: Chain A: P.43, G.44, E.68, 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.5 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A 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:G.448, B:D.449, B:D.449, A:G.95 TPP.12: 21 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: P.43, G.44, E.68, G.95 Ligands: MG.10 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D 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:E.480, C:M.481 Water bridges: C:C.403, C:G.448, C:D.449, C:D.449, C:N.476, D:G.95 TPP.16: 21 residues within 4Å: Chain C: P.43, G.44, E.68, G.95 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: MG.14 16 PLIP interactions: 15 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:D.449, D:G.450, D:A.451, D:N.476, D:E.480, D:M.481 Water bridges: D:C.403, D:G.448, D:D.449, D:D.449, C:G.95

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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.83, A:R.173, A:S.176 Water bridges: A:T.84, A:L.85 GOL.8: 7 residues within 4Å: Chain B: S.83, T.84, P.112, R.173, S.176, R.235, Y.236 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.176 Water bridges: B:S.83, B:T.84, B:T.84, B:L.85 GOL.9: 6 residues within 4Å: Chain B: H.63, Q.435, C.436, L.465, G.466, I.467 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.63 Water bridges: B:Q.435, B:G.439, B:G.440 GOL.13: 7 residues within 4Å: Chain C: S.83, T.84, P.112, R.173, S.176, R.235, Y.236 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.83, C:R.173, C:S.176 Water bridges: C:L.85 GOL.17: 7 residues within 4Å: Chain D: S.83, T.84, P.112, R.173, S.176, R.235, Y.236 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.176 Water bridges: D:S.83, D:T.84, D:T.84, D:L.85 GOL.18: 6 residues within 4Å: Chain D: H.63, Q.435, C.436, L.465, G.466, I.467 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.63 Water bridges: D:Q.435, D:G.439, D:G.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Versees, W. et al., The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 A resolution. Implications for its catalytic and regulatory mechanism. Febs J. (2007)

Release Date

2007-05-29

Peptides

PHENYL-3-PYRUVATE DECARBOXYLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PHENYL-3-PYRUVATE DECARBOXYLASE

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