SMTL ID : 8vha.2 (1 other biounit)

Crystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 7 residues within 4Å: Chain A: V.271, M.275, W.283, Q.293, S.296 Chain B: M.275, S.296 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.293, A:S.296 Water bridges: B:S.296, B:S.296

1 x EE1: (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid(Non-covalent)

EE1.2: 33 residues within 4Å: Chain A: E.33, K.88, A.90, T.91, I.92, T.93, R.98, S.110, N.112, R.125, D.291, L.304, G.305, A.323, A.324, H.325, G.326, T.327, V.328, T.329, R.330, H.331, T.343, N.344, D.391 Chain B: K.228, I.231, L.266, D.268, D.269, Q.273, K.276 Ligands: CA.3 28 PLIP interactions: 22 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.88, A:T.91, A:T.91, A:T.93, A:T.93, A:R.98, A:S.110, A:N.112, A:R.125, A:H.325, A:G.326, A:G.326, A:T.327, A:V.328, A:T.329, A:N.344, A:N.344, B:Q.273 Water bridges: A:T.91, A:L.304, A:R.330, B:D.268, B:D.268, B:D.269 Salt bridges: A:H.331, B:K.228, B:K.276 pi-Stacking: A:H.325

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.291, D.295 Chain B: D.268 Ligands: EE1.2 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.3 CA.6: 3 residues within 4Å: Chain A: D.268 Chain B: D.291, D.295 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.268, H2O.3, H2O.7, H2O.8, H2O.8

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

NDP.4: 15 residues within 4Å: Chain B: T.91, I.92, T.93, R.98, 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: 17 interactions with chain B Hydrogen bonds: B:T.93, B:R.98, B:H.325, B:T.327, B:V.328, B:T.329, B:N.344, B:N.344 Water bridges: B:T.93, B:R.98, B:R.330, B:H.331, B:H.331, B:K.390, B:K.390 Salt bridges: B:R.330, B:H.331

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: K.81, I.118, L.119, C.313, P.314, D.315, T.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.315, B:D.315

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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