SMTL ID : 6efh.1

Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

homo-dimer

Ligands

2 x PY0: (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate

PY0.1: 8 residues within 4Å: Chain A: H.92, C.221, H.225, G.286, A.287, L.288, H.310, S.311 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.288 Hydrogen bonds: A:H.310, A:H.310, A:S.311, A:S.311 Salt bridges: A:H.92, A:H.225 PY0.5: 9 residues within 4Å: Chain B: H.92, S.159, C.221, H.225, G.286, A.287, L.288, H.310, S.311 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.92 Hydrogen bonds: B:H.92, B:A.287, B:S.311 Salt bridges: B:H.92, B:H.225, B:H.310

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 21 residues within 4Å: Chain A: G.389, T.390, G.413, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Chain B: P.26, G.27, D.28, E.51, V.76 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.415, A:L.449, A:Y.474, A:Y.474 Hydrogen bonds: A:T.390, A:G.413, A:I.415, A:G.443, A:G.443, A:G.445, A:S.446, A:N.471, A:N.471, A:T.475, A:I.476 TPP.6: 21 residues within 4Å: Chain A: P.26, G.27, E.51, V.76 Chain B: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Ligands: MG.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.415, B:I.415, B:L.449, B:Y.474, B:Y.474 Hydrogen bonds: B:T.390, B:G.413, B:I.415, B:G.443, B:G.443, B:D.444, B:G.445, B:S.446, B:T.475, B:I.476

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.444, N.471, G.473, T.475 Ligands: TPP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.444, A:G.473 MG.7: 6 residues within 4Å: Chain B: G.443, D.444, L.469, N.471, G.473 Ligands: TPP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.444, B:G.473

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 7 residues within 4Å: Chain A: F.74, L.111, F.122, T.123, H.126, S.130, M.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kutter, S. et al., The crystal structures of pyruvate decarboxylase from Kluyveromyces lactis in the absence of ligands and in the presence of the substrate surrogate pyruvamide. To be Published

Release Date

2018-08-29

Peptides

Pyruvate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyruvate decarboxylase

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