SMTL ID : 6l59.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

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

ATP.1: 10 residues within 4Å: Chain A: I.18, H.266, G.267, T.268, A.269, P.270, D.271, A.278, N.279, D.320 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.267, A:A.269, A:D.271, A:N.279, A:N.279 pi-Stacking: A:H.266 ATP.3: 12 residues within 4Å: Chain B: I.29, P.255, G.256, N.276, T.277, G.278, K.279, S.280, I.281, A.287, N.288, D.329 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.276, B:T.277, B:T.277, B:G.278, B:K.279, B:S.280, B:S.280, B:N.288, B:N.288 Water bridges: B:E.83, B:T.272, B:A.291, A:N.214 Salt bridges: B:K.279, B:K.279

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.233, S.236, 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.4: 3 residues within 4Å: Chain B: N.81, R.275 Ligands: CIT.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.275, H2O.2, H2O.5

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

CIT.5: 13 residues within 4Å: Chain A: K.176, N.178, I.179 Chain B: N.81, T.84, S.94, N.96, R.100, R.131, Y.138, N.242, R.275 Ligands: MG.4 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.81, B:S.94, B:N.96, B:R.100, B:R.100, B:Y.138, B:N.242, A:N.178 Water bridges: B:T.84, B:T.84, B:R.131 Salt bridges: B:R.100, B:R.100, B:R.131, B:R.275, B:R.275, A:K.176

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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