SMTL ID : 8bay.1 (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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: W.245, E.247 No protein-ligand interaction detected (PLIP) GOL.2: 3 residues within 4Å: Chain A: N.357, E.361, I.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.357, A:N.357, A:E.361 GOL.9: 1 residues within 4Å: Chain B: R.314 No protein-ligand interaction detected (PLIP)

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

NDP.3: 19 residues within 4Å: Chain A: T.75, I.76, T.77, R.82, N.96, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, S.326, T.327, N.328, D.375 Ligands: QDC.4, QD8.5 16 PLIP interactions: 16 interactions with chain A 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:T.311, A:V.312, A:T.313, A:N.328, A:N.328 Water bridges: A:R.314 Salt bridges: A:R.314, A:H.315 NDP.8: 23 residues within 4Å: Chain A: D.253, 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, T.313, R.314, N.328, D.375 Ligands: QDC.10, QD8.11 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.72, B:T.75, 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:T.313, B:T.313, B:T.313, B:R.314, B:N.328 Salt bridges: B:R.314 pi-Cation interactions: B:R.314

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.3, QD8.5, CA.7 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.139, A:Y.139, B:I.215 Hydrogen bonds: A:S.94, A:N.96, B:K.212 Water bridges: A:T.77 Salt bridges: A:R.100, A:R.109 QDC.10: 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: CA.6, NDP.8, QD8.11 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.139, B:Y.139 Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:A.308, A:K.212 Water bridges: B:R.109 Salt bridges: B:R.100, B:R.109

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

QD8.5: 13 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, D.252 Ligands: NDP.3, QDC.4, CA.7 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.139, A:Y.139 Hydrogen bonds: A:S.94, A:N.96, B:K.212 Water bridges: A:T.77 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: CA.6, NDP.8, QDC.10 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.139, B:Y.139, A:I.215 Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:A.308, A:K.212 Water bridges: B:R.109 Salt bridges: B:R.100, B:R.109

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.3, H2O.4 CA.7: 5 residues within 4Å: Chain A: D.275, D.279 Chain B: D.252 Ligands: QDC.4, QD8.5 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.275, B:D.252, H2O.1, H2O.1, QD8.5

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
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic

Related Entries With Identical Sequence