SMTL ID : 2wvg.3 (4 other biounits)

Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x F: FLUORIDE ION(Non-covalent)

F.1: 5 residues within 4Å: Chain A: G.26, D.27, Y.28, T.72, H.114 No protein-ligand interaction detected (PLIP) F.5: 6 residues within 4Å: Chain B: G.26, D.27, Y.28, T.72, H.114 Ligands: TPU.2 No protein-ligand interaction detected (PLIP)

2 x TPU: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TPU.2: 23 residues within 4Å: Chain A: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, N.467, G.469, Y.470, T.471, I.472, E.473 Chain B: A.25, G.26, E.50, V.75, H.114 Ligands: MG.3, F.5 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.415, A:Y.470, A:Y.470, A:I.472 Hydrogen bonds: A:D.390, A:G.413, A:I.415, A:G.439, A:G.441, A:S.442, A:N.467, A:T.471, A:I.472 Water bridges: A:S.391, A:D.440, A:D.440, A:S.442, A:S.442, B:E.50 TPU.6: 21 residues within 4Å: Chain A: A.25, G.26, E.50, V.75, H.114 Chain B: G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, N.467, G.469, Y.470, T.471, I.472, E.473 Ligands: MG.4 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.415, B:Y.470, B:Y.470, B:I.472, A:V.75 Hydrogen bonds: B:D.390, B:G.413, B:I.415, B:G.439, B:G.441, B:S.442, B:N.467, B:T.471, B:I.472 Water bridges: B:Y.290, B:S.391, B:D.440, B:D.440, B:S.442, B:S.442, A:E.50

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.440, N.467, G.469 Ligands: TPU.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.440, A:G.469, H2O.21 MG.4: 4 residues within 4Å: Chain B: D.440, N.467, G.469 Ligands: TPU.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.440, B:G.469, H2O.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pei, X.Y. et al., Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase from Zymomonas Mobilis. Biochemistry (2010)

Release Date

2010-02-09

Peptides

PYRUVATE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

PYRUVATE DECARBOXYLASE

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