SMTL ID : 3map.1

Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 21 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Ligands: ICT.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.75, A:T.75, A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:G.310, A:G.310, A:T.311, A:V.312, A:T.313, A:T.313, A:N.328, A:N.328 Salt bridges: A:R.314, A:H.315 NAP.3: 23 residues within 4Å: Chain A: 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, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328, D.375 Ligands: ICT.4 19 PLIP interactions: 17 interactions with chain B, 2 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:R.82, B:N.96, B:H.309, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, A:K.260 Salt bridges: B:R.314, B:H.315, A:K.260 pi-Stacking: B:H.309

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 7 residues within 4Å: Chain A: T.77, S.94, N.96, G.97, R.100, R.109 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.77, A:S.94, A:N.96, A:G.97 Salt bridges: A:R.100, A:R.100, A:R.109 ICT.4: 6 residues within 4Å: Chain B: T.77, S.94, N.96, G.97, R.100 Ligands: NAP.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.77 Hydrogen bonds: B:S.94, B:N.96, B:G.97 Salt bridges: B:R.100, B:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, B. et al., Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H. Cell Res. (2010)

Release Date

2010-11-10

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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