SMTL ID : 9h4e.1

trans-aconitate decarboxylase Tad1- wild type binding with glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL

GOL.1: 3 residues within 4Å: Chain A: Q.152, R.360, W.365 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.360 GOL.3: 4 residues within 4Å: Chain B: Q.152, R.360, T.362, W.365 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.362 GOL.4: 7 residues within 4Å: Chain C: T.151, Q.152, T.155, R.360, G.361, T.362, W.365 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.152, C:R.360, C:R.360 GOL.5: 5 residues within 4Å: Chain D: T.151, Q.152, R.360, T.362, W.365 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.365

1 x MG: MAGNESIUM ION

MG.2: 7 residues within 4Å: Chain A: A.240, A.241, G.242, H.272, E.359, R.360 Chain D: R.213 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.272, A:E.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, L. et al., Mechanistic and structural insights into the itaconate-producing trans -aconitate decarboxylase Tad1. Pnas Nexus (2025)

Release Date

2025-03-19

Peptides

Trans-aconitate decarboxylase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

Trans-aconitate decarboxylase 1