SMTL ID : 5gre.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.230, D.234 Chain B: D.215 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.230, A:D.234, B:D.215, H2O.1 MG.3: 4 residues within 4Å: Chain B: N.78, R.272 Ligands: ADP.2, CIT.4 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.272, H2O.2

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 18 residues within 4Å: Chain A: Y.204, T.207 Chain B: I.26, N.78, E.80, P.252, G.253, R.272, N.273, T.274, G.275, K.276, S.277, I.278, A.284, N.285, D.326 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.273, B:T.274, B:T.274, B:G.275, B:K.276, B:S.277, B:N.285, B:N.285 Water bridges: B:K.276, B:K.276, B:S.277, B:A.288 Salt bridges: B:K.276, B:K.276

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

CIT.4: 13 residues within 4Å: Chain A: K.173, N.175, I.176 Chain B: N.78, T.81, S.91, N.93, R.97, R.128, Y.135, N.239, R.272 Ligands: MG.3 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.78, B:S.91, B:N.93, B:R.97, B:R.97, B:Y.135, B:N.239, A:N.175, A:D.206 Water bridges: B:T.81, B:T.81, B:R.128, B:R.272 Salt bridges: B:R.97, B:R.97, B:R.128, B:R.272, B:R.272, A:K.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, T. et al., Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase. Sci Rep (2017)

Release Date

2017-02-15

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

Related Entries With Identical Sequence