SMTL ID : 5yzi.1

Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase complexed with Cadmium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

3 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: D.275, D.279, A.308 Chain B: D.252 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.275, B:D.252 CD.3: 5 residues within 4Å: Chain A: D.252 Chain B: R.109, D.275, D.279, A.308 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.275 CD.4: 2 residues within 4Å: Chain B: C.245, E.247 No protein-ligand interaction detected (PLIP)

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

NAP.2: 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 24 PLIP interactions: 6 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:D.253, B:D.253, B:Q.257, B:Q.257, A:T.75, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:N.96, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328 Water bridges: B:D.253, A:T.313, A:T.313, A:A.331 Salt bridges: B:K.260, A:H.315 NAP.5: 25 residues within 4Å: Chain A: 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, E.306, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.72, B:T.75, B:T.77, B:T.77, B:T.77, B:R.82, B:N.96, B:E.306, B:A.308, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Salt bridges: B:H.315, A:K.260

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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