SMTL ID : 5yvt.1

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.230, D.234 Chain B: D.215 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.230, A:D.234, B:D.215, H2O.1, H2O.1, H2O.4

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 19 residues within 4Å: Chain A: I.15, K.69, L.72, K.73, T.74, N.84, L.243, E.260, S.261, V.262, H.263, G.264, T.265, A.266, D.268, I.269, A.275, N.276, D.317 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.69, A:L.72, A:T.74, A:T.74, A:N.84, A:E.260, A:G.264, A:T.265, A:A.266, A:D.268, A:N.276, A:N.276 NAI.3: 19 residues within 4Å: Chain A: N.175, Y.204, D.206, T.207 Chain B: I.26, E.80, T.81, P.252, G.253, R.272, N.273, T.274, G.275, K.276, S.277, I.278, A.284, N.285, D.326 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:R.272 Hydrogen bonds: B:E.80, B:T.81, B:T.81, B:N.273, B:T.274, B:G.275, B:K.276, B:S.277, B:S.277, B:S.277, B:N.285, B:N.285, A:N.175, A:D.206 Water bridges: B:T.269, B:A.288 pi-Stacking: A:Y.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Insights into the inhibitory mechanisms of NADH on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase. Sci Rep (2018)

Release Date

2018-03-14

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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