SMTL ID : 5i95.1

Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer bound to NADPH and alpha-Ketoglutaric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 23 residues within 4Å: Chain A: K.74, A.76, T.77, I.78, T.79, R.84, N.98, L.289, A.309, H.310, G.311, T.312, V.313, T.314, R.315, H.316, T.328, N.329 Chain B: L.251, D.254, Q.258, K.261 Ligands: AKG.8 29 PLIP interactions: 22 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:K.74, A:T.77, A:T.79, A:T.79, A:R.84, A:R.84, A:N.98, A:N.98, A:H.310, A:G.311, A:G.311, A:T.312, A:V.313, A:R.315, A:N.329, B:D.254, B:Q.258, B:Q.258 Water bridges: A:T.77, A:T.314, A:R.315, A:R.315, A:A.332, B:D.254, B:D.254, B:K.261 Salt bridges: A:R.315, A:H.316, B:K.261 NDP.9: 23 residues within 4Å: Chain A: L.251, D.254, Q.258, K.261 Chain B: K.74, A.76, T.77, I.78, T.79, R.84, N.98, L.289, A.309, H.310, G.311, T.312, V.313, T.314, R.315, H.316, T.328, N.329 Ligands: AKG.16 27 PLIP interactions: 20 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:K.74, B:T.77, B:T.79, B:T.79, B:T.79, B:R.84, B:R.84, B:N.98, B:N.98, B:G.311, B:G.311, B:T.312, B:V.313, B:R.315, B:N.329, B:N.329, A:Q.258, A:Q.258 Water bridges: B:R.315, B:A.332, A:D.254, A:D.254, A:D.254, A:K.261 Salt bridges: B:R.315, B:H.316, A:K.261

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.276 Chain B: K.213, D.253 Ligands: AKG.8 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.253, A:D.276, H2O.1, H2O.3 CA.10: 4 residues within 4Å: Chain A: K.213, D.253 Chain B: D.276 Ligands: AKG.16 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.276, A:D.253, H2O.24, H2O.25

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: F.158, W.169 Chain B: F.146, V.147, A.148, D.149, R.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.147, B:D.149, B:R.150 GOL.4: 3 residues within 4Å: Chain A: F.110, E.112, Y.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.112 Water bridges: A:E.112, A:V.295, A:R.339 GOL.5: 6 residues within 4Å: Chain A: V.363, E.366, T.367, S.370, N.406 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.370 Water bridges: A:N.406 GOL.6: 6 residues within 4Å: Chain A: K.362, V.363, E.366, A.410, R.413 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.362, A:R.413 GOL.11: 7 residues within 4Å: Chain A: F.146, V.147, A.148, D.149, R.150 Chain B: F.158, W.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.147, A:D.149, A:R.150 GOL.12: 3 residues within 4Å: Chain B: F.110, E.112, Y.200 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.112, B:T.293, B:V.295 GOL.13: 6 residues within 4Å: Chain B: V.363, E.366, T.367, S.370, N.406 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.370 Water bridges: B:N.406 GOL.14: 6 residues within 4Å: Chain B: K.362, V.363, E.366, A.410, R.413 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.362, B:E.366, B:R.413

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain A: P.325, K.375, L.389, F.393 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.389, A:F.393 Hydrogen bonds: A:P.325 Salt bridges: A:K.375 ACT.15: 4 residues within 4Å: Chain B: P.325, K.375, L.389, F.393 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.389, B:F.393 Hydrogen bonds: B:P.325 Salt bridges: B:K.375

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

AKG.8: 12 residues within 4Å: Chain A: T.79, S.96, N.98, R.111, R.134, D.276, A.309 Chain B: K.213, I.216, D.253 Ligands: NDP.1, CA.2 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.79, A:S.96, A:N.98, B:K.213 Water bridges: A:G.99, A:R.134, A:D.276 Salt bridges: A:R.111, A:R.134 AKG.16: 12 residues within 4Å: Chain A: K.213, I.216, D.253 Chain B: T.79, S.96, N.98, R.111, R.134, D.276, A.309 Ligands: NDP.9, CA.10 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.96, B:N.98, A:K.213 Water bridges: B:T.79, B:T.79, B:G.99, B:R.134 Salt bridges: B:R.111, B:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, K. et al., AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations. Cancer Discov (2017)

Release Date

2017-03-01

Peptides

Isocitrate dehydrogenase [NADP], mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Isocitrate dehydrogenase [NADP], mitochondrial