SMTL ID : 8vhd.2 (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

1 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.1: 13 residues within 4Å: Chain A: T.93, S.110, N.112, R.116, R.125, Y.155, D.291, A.324 Chain B: K.228, I.231, D.268 Ligands: NAP.3, CA.5 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.110, A:N.112, A:Y.155, B:K.228 Water bridges: A:T.93, A:R.116, A:R.116, A:R.125, B:T.230, B:D.268, B:D.268 Salt bridges: A:R.116, A:R.125, B:K.228

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.48, V.51, E.52, L.53, L.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.48, A:L.53 Water bridges: A:L.55 GOL.7: 4 residues within 4Å: Chain B: K.74, T.114, N.117, I.118 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.117 GOL.8: 2 residues within 4Å: Chain B: Y.335, F.411 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.335 Water bridges: B:Y.335

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

NAP.3: 23 residues within 4Å: Chain A: K.88, A.90, T.91, T.93, R.98, N.112, L.304, G.305, A.323, H.325, G.326, T.327, V.328, T.329, R.330, H.331, T.343, N.344 Chain B: L.266, D.269, Q.273, K.276 Ligands: ICT.1 30 PLIP interactions: 23 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.91, A:T.93, A:T.93, A:T.93, A:R.98, A:R.98, A:N.112, A:E.322, A:G.326, A:T.327, A:V.328, A:R.330, A:N.344, A:N.344, B:D.269, B:D.269, B:Q.273 Water bridges: A:T.91, A:L.304, A:T.329, A:T.329, A:T.329, A:R.330, A:H.331, A:A.347, B:D.269, B:K.276, B:K.276 Salt bridges: A:H.331, B:K.276 NAP.6: 19 residues within 4Å: Chain B: K.88, A.90, T.91, I.92, T.93, 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 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.91, B:T.93, B:T.93, B:R.98, B:A.323, B:H.325, B:T.327, B:V.328, B:T.329, B:R.330, B:N.344, B:N.344 Water bridges: B:H.325, B:H.325, B:H.331, A:D.269 Salt bridges: B:H.331

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

IOD.4: 3 residues within 4Å: Chain A: E.340, T.341, F.411 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain B: T.341, N.409, F.411 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.291, D.295 Chain B: D.268 Ligands: ICT.1 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.291, B:D.268, H2O.1, H2O.2 CA.10: 3 residues within 4Å: Chain A: D.268 Chain B: D.291, D.295 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.5, H2O.8, H2O.11

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
C

B
D

Isocitrate dehydrogenase [NADP] cytoplasmic

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