SMTL ID : 5yzh.1

Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 24 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Chain B: L.250, D.253, Q.257, K.260 31 PLIP interactions: 22 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:A.308, A:G.310, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328, B:D.253, B:Q.257 Water bridges: A:T.77, A:T.313, A:T.313, A:R.314, A:R.314, A:H.315, A:A.331, A:D.375, B:R.249, B:D.253, B:D.253, B:D.253, B:K.260, B:K.260 Salt bridges: A:H.315, B:K.260 NAP.3: 24 residues within 4Å: Chain A: L.250, D.253, Q.257, K.260 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 29 PLIP interactions: 22 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:A.308, B:H.309, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, A:D.253, A:Q.257 Water bridges: B:T.77, B:R.109, B:T.313, B:R.314, B:R.314, B:H.315, B:A.331, A:D.253, A:D.253, A:D.253, A:Q.257 Salt bridges: B:H.315, A:K.260

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.126, P.206, E.262, G.263, G.264, F.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.262 Water bridges: A:E.262, A:E.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, H.J. et al., NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione. J. Biol. Inorg. Chem. (2018)

Release Date

2018-07-04

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic

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