SMTL ID : 4l03.1 (1 other biounit)

Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 25 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 Ligands: AKG.4 28 PLIP interactions: 18 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:K.72, 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, B:D.253, B:Q.257 Water bridges: A:T.75, B:D.253, B:D.253, B:D.253, B:D.253, B:Q.257, B:K.260, B:K.260 Salt bridges: A:R.314, A:H.315, B:K.260 pi-Stacking: A:H.309 NAP.5: 25 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 Ligands: AKG.7 31 PLIP interactions: 22 interactions with chain B, 9 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:E.306, B:G.310, B:T.311, B:V.312, B:T.313, B:T.313, B:N.328, B:N.328, A:Q.257 Water bridges: B:R.314, B:R.314, B:A.331, A:D.253, A:D.253, A:D.253, A:D.253, A:Q.257, A:K.260, A:K.260 Salt bridges: B:R.314, B:H.315, A:K.260 pi-Stacking: B:H.309

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.275, D.279 Chain B: D.252 Ligands: AKG.4 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.252, A:D.275, A:D.279, H2O.1, H2O.1 CA.6: 4 residues within 4Å: Chain A: D.252 Chain B: D.275, D.279 Ligands: AKG.7 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.252, B:D.275, B:D.279, H2O.10, H2O.10

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: D.273, V.276, Q.277 Chain B: Y.272, D.273, V.276, Q.277 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.273, B:Q.277, A:Q.277

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.4: 13 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, D.275, A.308 Chain B: K.212, I.215, D.252 Ligands: NAP.1, CA.2 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:K.212, A:T.77, A:S.94, A:N.96 Water bridges: B:T.214, B:D.252, B:D.252, A:R.100, A:R.100, A:R.132 Salt bridges: A:R.100, A:R.109, A:R.132 AKG.7: 13 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, D.275, A.308 Ligands: NAP.5, CA.6 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.94, B:N.96, A:K.212 Water bridges: B:T.77, B:T.77, B:T.77, B:R.100, B:R.109, B:R.132, B:R.132, B:D.279, B:A.308, A:T.214 Salt bridges: B:R.100, B:R.109, B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rendina, A.R. et al., Mutant IDH1 Enhances the Production of 2-Hydroxyglutarate Due to Its Kinetic Mechanism. Biochemistry (2013)

Release Date

2013-07-17

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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