SMTL ID : 7cp1.1

Crystal structure of isocitrate lyase in complex with succinate and itaconate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-tetramer

Ligands

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 7 residues within 4Å: Chain A: W.93, D.108, D.153, R.228, N.313, T.347 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.93, A:T.347 Hydrogen bonds: A:Y.89, A:Y.89, A:N.313, A:T.347, A:T.347 Water bridges: A:D.108, A:R.228, A:R.228, A:R.228, A:R.228 Salt bridges: A:R.228 SIN.5: 7 residues within 4Å: Chain C: W.93, D.108, D.153, R.228, N.313, T.347 Ligands: MG.6 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.93, C:T.347 Hydrogen bonds: C:Y.89, C:N.313, C:T.347 Water bridges: C:R.228, C:R.228, C:R.228, C:R.228, D:Q.394 Salt bridges: C:R.228

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: W.93, D.108, D.153, E.155 Ligands: SIN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.108, A:D.153, A:E.155, H2O.4 MG.4: 6 residues within 4Å: Chain B: G.92, W.93, D.108, D.153, E.155 Ligands: ITN.3 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.108, B:D.153, B:E.155, H2O.15 MG.6: 5 residues within 4Å: Chain C: W.93, D.108, D.153, E.155 Ligands: SIN.5 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.108, C:D.153, C:E.155, H2O.28 MG.8: 6 residues within 4Å: Chain D: G.92, W.93, D.108, D.153, E.155 Ligands: ITN.7 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.108, D:D.153, D:E.155, H2O.39

2 x ITN: 2-methylidenebutanedioic acid(Non-covalent)

ITN.3: 10 residues within 4Å: Chain B: W.93, D.108, D.153, R.228, E.285, N.313, P.316, T.347, L.348 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.93, B:T.347, B:L.348 Hydrogen bonds: B:R.228, B:N.313, B:T.347 Water bridges: B:D.153, B:R.228, B:R.228 Salt bridges: B:R.228 ITN.7: 10 residues within 4Å: Chain D: W.93, D.108, D.153, R.228, E.285, N.313, P.316, T.347, L.348 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.93, D:T.347, D:L.348 Hydrogen bonds: D:Y.89, D:R.228, D:N.313 Water bridges: D:R.228, D:R.228 Salt bridges: D:R.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, S. et al., Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism. Plos One (2021)

Release Date

2021-05-19

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Isocitrate lyase