SMTL ID : 8zk8.1

Crystal structure of the Decarboxylase KDC4427 mutant E468L in complex with indole-3-pyruvic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 25 residues within 4Å: Chain A: Q.397, 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, V.91, H.130 Ligands: MG.2, 3IO.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.424, A:L.454, A:L.482 Hydrogen bonds: A:T.399, A:G.422, A:I.424, A:G.448, A:G.450, A:A.451, A:G.478, A:T.480, A:V.481 Water bridges: A:S.400, A:D.449 TPP.4: 24 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: 3IO.3, MG.5 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.424, B:I.424, B:L.454, B:Y.479, B:L.482 Hydrogen bonds: B:T.399, B:G.422, B:I.424, B:G.448, B:D.449, B:G.450, B:A.451, B:N.476, B:N.476, B:T.480, B:T.480, B:V.481 Water bridges: B:S.400, B:D.449, B:D.449, A:E.66

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.449, N.476, G.478 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.5: 5 residues within 4Å: Chain B: D.449, N.476, G.478, T.480 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.449, B:G.478, H2O.11

2 x 3IO: 3-(1H-INDOL-3-YL)-2-OXOPROPANOIC ACID(Non-covalent)

3IO.3: 14 residues within 4Å: Chain A: P.41, G.42, D.43, Y.44, T.88, H.129, H.130 Chain B: T.304, Q.397, F.402, G.422, L.482, I.485 Ligands: TPP.4 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.43, B:I.485 Hydrogen bonds: A:P.41, A:D.43, A:Y.44, B:Q.397 Salt bridges: A:H.130 pi-Stacking: A:H.129, A:H.129 Water bridges: B:T.304, B:T.304 3IO.6: 13 residues within 4Å: Chain A: T.304, Q.397, F.402, G.422, L.482, I.485 Chain B: P.41, G.42, D.43, T.88, H.129, H.130 Ligands: TPP.1 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:D.43, A:F.402, A:I.485 Hydrogen bonds: B:D.43, B:D.43, B:T.88, A:Q.397 Salt bridges: B:H.129, B:H.130 pi-Stacking: B:H.129, B:H.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, S. et al., Crystal structure of the Decarboxylase KDC4427 mutant E468L in complex with indole-3-pyruvic acid. 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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