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

Crystal Structure of IDH1 variant R132C S280F in complex with NADPH, Ca2+ and 3-butyl-2-oxoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: W.245, E.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.247, A:R.249 GOL.3: 3 residues within 4Å: Chain A: N.357, E.360, E.361 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.360, A:E.361 GOL.7: 2 residues within 4Å: Chain B: W.245, E.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.247, B:R.249 GOL.9: 3 residues within 4Å: Chain B: N.357, E.360, E.361 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.360, B:E.360, B:E.361, B:E.361

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

NDP.2: 22 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, 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: D.253 Ligands: QDC.4, QD8.5 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.75, 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:T.311, A:V.312, A:N.328, A:N.328 Water bridges: A:A.331 Salt bridges: A:R.314, B:K.260 pi-Stacking: A:H.309, A:H.309 NDP.8: 22 residues within 4Å: Chain A: D.253 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: QDC.10, QD8.11 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:A.308, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Water bridges: B:A.331 Salt bridges: B:R.314, A:K.260 pi-Stacking: B:H.309, B:H.309

2 x QDC: (R)-3-butyl-2-oxopentanedioic acid(Non-covalent)

QDC.4: 14 residues within 4Å: Chain A: T.77, S.94, N.96, G.97, R.100, R.109, Y.139, D.275 Chain B: K.212, I.215, D.252 Ligands: NDP.2, QD8.5, CA.6 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.215, A:Y.139 Hydrogen bonds: B:K.212, A:T.77, A:S.94, A:N.96 Water bridges: B:D.252 Salt bridges: A:R.100, A:R.109 QDC.10: 14 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, G.97, R.100, R.109, Y.139, D.275 Ligands: NDP.8, QD8.11, CA.12 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.139, A:I.215 Hydrogen bonds: B:S.94, B:N.96, A:K.212 Water bridges: B:T.77 Salt bridges: B:R.100, B:R.109

2 x QD8: (S)-3-butyl-2-oxopentanedioic acid(Non-covalent)

QD8.5: 15 residues within 4Å: Chain A: T.77, S.94, N.96, G.97, R.100, R.109, Y.139, D.275, A.308 Chain B: K.212, I.215, D.252 Ligands: NDP.2, QDC.4, CA.6 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.215, A:Y.139, A:Y.139 Hydrogen bonds: B:K.212, A:T.77, A:S.94, A:N.96 Water bridges: B:D.252 Salt bridges: A:R.100, A:R.109 QD8.11: 15 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, G.97, R.100, R.109, Y.139, D.275, A.308 Ligands: NDP.8, QDC.10, CA.12 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.139, B:Y.139, A:I.215 Hydrogen bonds: B:S.94, B:N.96, A:K.212 Water bridges: B:T.77 Salt bridges: B:R.100, B:R.109

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.275, D.279 Chain B: D.252 Ligands: QDC.4, QD8.5 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.252, A:D.275, H2O.1, H2O.4 CA.12: 5 residues within 4Å: Chain A: D.252 Chain B: D.275, D.279 Ligands: QDC.10, QD8.11 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.252, B:D.275, H2O.5, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., Natural and synthetic 2-oxoglutarate derivatives are substrates for oncogenic variants of human isocitrate dehydrogenase 1 and 2. J.Biol.Chem. (2023)

Release Date

2022-11-02

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Isocitrate dehydrogenase [NADP] cytoplasmic

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