SMTL ID : 8gru.2 (1 other biounit)

Crystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ICT, NAD and Ca

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)(Non-covalent)

NAD.1: 21 residues within 4Å: Chain A: K.69, P.71, L.72, T.74, N.84, L.243, G.244, E.260, V.262, H.263, G.264, T.265, A.266, D.268, I.269, N.276, D.317 Chain B: N.186, I.215, N.218 Ligands: ICT.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.69, A:K.69, A:L.72, A:T.74, A:T.74, A:G.264, A:G.264, A:T.265, A:A.266, A:N.276, A:N.276, B:N.186 NAD.4: 13 residues within 4Å: Chain A: Y.204, T.207, L.210 Chain B: L.29, A.254, G.255, H.275, P.276, F.277, A.278, A.286, N.287, D.328 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.207, B:F.277, B:F.277, B:N.287, B:N.287 Salt bridges: B:H.275, B:H.275 pi-Stacking: B:F.277, B:F.277

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: R.98, D.230, D.234, V.262 Chain B: D.217 Ligands: ICT.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.230, B:D.217

1 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.3: 13 residues within 4Å: Chain A: T.74, S.82, N.84, R.88, R.98, R.119, Y.126, D.230 Chain B: K.184, N.186, D.217 Ligands: NAD.1, CA.2 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.82, A:N.84, B:K.184, B:N.186 Salt bridges: A:R.88, A:R.98, A:R.119, A:R.119, B:K.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction. J.Biol.Chem. (2022)

Release Date

2022-11-30

Peptides

Human IDH3 alpha subunit: A
Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Human IDH3 alpha subunit

Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial

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