SMTL ID : 8zk7.1

Crystal structure of the Decarboxylase KDC4427 mutant E468L from Enterobacter sp. CGMCC 5087

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 residues within 4Å: Chain A: G.398, T.399, G.422, S.423, I.424, G.448, D.449, G.450, A.451, L.454, N.476, G.478, Y.479, T.480, V.481, L.482 Chain B: V.40, P.41, G.42, E.66, T.88, V.91, H.130 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.424, A:L.454, A:Y.479, A:V.481, A:L.482 Hydrogen bonds: A:T.399, A:G.422, A:I.424, A:D.449, A:G.450, A:A.451, A:N.476, A:T.480, A:V.481 Water bridges: A:S.400, A:G.448, A:G.448, A:D.449 TPP.3: 23 residues within 4Å: Chain A: V.40, P.41, G.42, E.66, V.91, H.130 Chain B: G.398, T.399, G.422, S.423, I.424, G.448, D.449, G.450, A.451, L.454, N.476, G.478, Y.479, T.480, V.481, L.482 Ligands: MG.4 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.424, B:L.454, B:Y.479, B:V.481, B:L.482 Hydrogen bonds: B:T.399, B:G.422, B:I.424, B:D.449, B:G.450, B:A.451, B:N.476, B:T.480, B:T.480, B:V.481 Water bridges: B:S.400, B:G.448, B:D.449, A:E.66

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.449, N.476, G.478, T.480 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.449, A:G.478, H2O.2 MG.4: 5 residues within 4Å: Chain B: D.449, G.450, N.476, G.478 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.449, B:G.478, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, S. et al., Crystal structure of the Decarboxylase KDC4427 mutant E468L from Enterobacter sp. CGMCC 5087. To Be Published

Release Date

2025-05-21

Peptides

Indolepyruvate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Indolepyruvate decarboxylase

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