SMTL ID : 6l57.1

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT , Mg and ATP binding at allosteric site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.233, D.237 Chain B: D.218 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.233, A:D.233, A:D.237, B:D.218 MG.3: 3 residues within 4Å: Chain B: N.81, R.275 Ligands: CIT.2 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.275, H2O.3, H2O.4

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 12 residues within 4Å: Chain A: K.176, N.178 Chain B: N.81, T.84, S.94, N.96, R.100, R.131, Y.138, N.242, R.275 Ligands: MG.3 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:N.178, B:N.81, B:S.94, B:N.96, B:R.100, B:R.100, B:Y.138, B:R.275 Water bridges: A:K.176, A:D.209, B:T.84, B:T.84 Salt bridges: A:K.176, B:R.100, B:R.100, B:R.131, B:R.275, B:R.275

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 12 residues within 4Å: Chain A: T.210 Chain B: I.29, P.255, N.276, T.277, G.278, K.279, S.280, I.281, A.287, N.288, D.329 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.276, B:T.277, B:G.278, B:S.280, B:S.280, B:S.280, B:N.288, B:N.288, A:T.210 Water bridges: B:K.279, B:K.279 Salt bridges: B:K.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, P. et al., Molecular mechanism of the dual regulatory roles of ATP on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase. Sci Rep (2020)

Release Date

2020-04-29

Peptides

Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial: A
Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial

Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial

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