SMTL ID : 3inm.2 (1 other biounit)

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 24 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, N.328 Chain B: L.250, D.253, Q.257, K.260 Ligands: AKG.2, NA.4 24 PLIP interactions: 17 interactions with chain A, 7 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:H.309, A:G.310, A:G.310, A:T.311, A:V.312, A:R.314, A:R.314, A:N.328, B:D.253, B:Q.257 Water bridges: A:T.75, B:D.253, B:D.253, B:K.260, B:K.260 Salt bridges: A:H.315, B:K.260 NDP.6: 24 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, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, N.328 Ligands: AKG.7, NA.9 24 PLIP interactions: 7 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:Q.257, B:T.75, B:T.75, B:T.77, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:G.310, B:G.310, B:T.311, B:V.312, B:R.314, B:R.314, B:N.328, B:N.328 Water bridges: A:D.253, A:D.253, A:D.253, A:K.260, A:K.260 Salt bridges: A:K.260, B:H.315

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

AKG.2: 14 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, Y.139, D.275, A.308 Chain B: K.212, T.214, I.215, D.252 Ligands: NDP.1, CA.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.77, A:S.94, A:N.96, A:Y.139, A:A.308, B:K.212 Salt bridges: A:R.100, A:R.109 AKG.7: 14 residues within 4Å: Chain A: K.212, T.214, I.215, D.252 Chain B: T.77, S.94, N.96, R.100, R.109, Y.139, D.275, A.308 Ligands: NDP.6, CA.8 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:K.212, A:T.214, B:S.94, B:N.96, B:Y.139, B:A.308 Water bridges: B:T.77 Salt bridges: B:R.100, B:R.109

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: R.109, D.275, D.279 Chain B: D.252 Ligands: AKG.2 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, A:D.279, B:D.252, H2O.1, H2O.1 CA.8: 5 residues within 4Å: Chain A: D.252 Chain B: R.109, D.275, D.279 Ligands: AKG.7 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.275, B:D.279, A:D.252, H2O.3, H2O.4

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: R.314 Ligands: NDP.1 No protein-ligand interaction detected (PLIP) NA.9: 2 residues within 4Å: Chain B: R.314 Ligands: NDP.6 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: F.108, R.109, E.110, I.129, M.199, K.203, T.292 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.108, A:E.110, A:E.110, A:K.203, A:K.203, A:T.292 Water bridges: A:R.338 GOL.10: 7 residues within 4Å: Chain B: F.108, R.109, E.110, I.129, M.199, K.203, T.292 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.108, B:E.110, B:K.203, B:K.203 Water bridges: B:T.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dang, L. et al., Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature (2009)

Release Date

2009-11-24

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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