SMTL ID : 8vhd.1 (1 other biounit)

Crystal Structure of Human IDH1 R132Q in complex with NADPH and Isocitrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 20 residues within 4Å: Chain A: K.88, A.90, T.91, I.92, T.93, R.98, N.112, L.304, G.305, E.322, A.323, H.325, G.326, T.327, V.328, T.329, R.330, H.331, T.343, N.344 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.88, A:T.91, A:T.93, A:T.93, A:R.98, A:R.98, A:N.112, A:E.322, A:H.325, A:G.326, A:G.326, A:T.327, A:V.328, A:N.344 Water bridges: A:E.322, A:E.322, A:T.329, A:T.329, A:T.329, A:T.329, A:A.347 Salt bridges: A:R.330, A:H.331, B:K.276 NAP.5: 20 residues within 4Å: Chain B: K.88, A.90, T.91, I.92, T.93, R.98, N.112, A.323, A.324, H.325, G.326, T.327, V.328, T.329, R.330, H.331, S.342, T.343, N.344, D.391 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.91, B:T.93, B:T.93, B:R.98, B:R.98, B:N.112, B:A.324, B:T.327, B:V.328, B:R.330, B:N.344, B:N.344 Water bridges: B:T.329, B:R.330, B:I.346, A:D.269 Salt bridges: B:R.330, B:H.331

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: T.341, F.411 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain B: E.340, T.341, N.409 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.291, D.295 Chain B: D.268 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.291, A:D.295, B:D.268, H2O.7, H2O.8 CA.7: 2 residues within 4Å: Chain A: D.268 Chain B: D.291 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.268, B:D.291, H2O.9, H2O.15, H2O.15

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: K.81, L.119, C.313, P.314, D.315, T.318 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.315 Water bridges: B:D.315, B:T.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mealka, M. et al., Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. Nat Commun (2024)

Release Date

2024-04-24

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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