SMTL ID : 2qfx.1 (2 other biounits)

Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADPH, a-ketoglutarate and Ca(2+)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: R.124, D.291, D.295 Chain B: D.268 Ligands: AKG.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.268, A:D.291 CA.4: 5 residues within 4Å: Chain A: D.268 Chain B: R.124, D.291, D.295 Ligands: AKG.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.268, B:D.291, B:D.295

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 23 residues within 4Å: Chain A: K.87, A.89, T.90, I.91, T.92, R.97, N.111, L.304, G.305, E.322, H.325, G.326, T.327, V.328, T.329, R.330, H.331, T.343, N.344 Chain B: D.269, Q.273, K.276 Ligands: AKG.3 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.90, A:T.92, A:R.97, A:R.97, A:N.111, A:E.322, A:G.326, A:T.327, A:V.328, A:T.329, A:R.330, A:N.344, A:N.344, B:D.269, B:Q.273 Water bridges: A:T.92, A:A.347, B:L.266, B:D.269 Salt bridges: A:H.331, B:K.276 NDP.5: 22 residues within 4Å: Chain A: L.266, D.269, Q.273, K.276 Chain B: K.87, A.89, T.90, I.91, T.92, R.97, N.111, L.304, H.325, G.326, T.327, V.328, T.329, R.330, H.331, T.343, N.344 Ligands: AKG.6 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.90, B:T.92, B:T.92, B:R.97, B:R.97, B:N.111, B:N.111, B:G.326, B:G.326, B:T.327, B:V.328, B:T.329, B:R.330, B:N.344, B:N.344, A:Q.273 Water bridges: B:A.347 Salt bridges: B:H.331, A:K.276

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 13 residues within 4Å: Chain A: T.92, S.109, N.111, R.115, R.124, R.147, D.291, A.324 Chain B: K.228, T.230, D.268 Ligands: CA.1, NDP.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.109, A:N.111, B:K.228 Salt bridges: A:R.115, A:R.124, A:R.147 AKG.6: 12 residues within 4Å: Chain A: K.228, D.268 Chain B: T.92, S.109, N.111, R.115, R.124, R.147, D.291, A.324 Ligands: CA.4, NDP.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.92, B:S.109, B:N.111, A:K.228 Salt bridges: B:R.115, B:R.124, B:R.147 Water bridges: A:K.228, A:T.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, Y.J. et al., Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction. Protein Sci. (2008)

Release Date

2008-07-01

Peptides

Isocitrate dehydrogenase [NADP]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP]

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