SMTL ID : 8vh9.1

Crystal Structure of Human IDH1 R132Q in complex with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: T.93, S.110, N.112 Ligands: NDP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.93, A:S.110, A:S.110 GOL.2: 6 residues within 4Å: Chain A: M.215, S.218, V.310, V.319, R.354, H.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.218, A:S.218, A:K.361, A:K.361 GOL.3: 5 residues within 4Å: Chain A: S.22, G.23, G.24, E.52, D.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.22, A:G.24, A:D.54 GOL.6: 4 residues within 4Å: Chain B: M.215, S.218, H.358, K.361 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.218, B:S.218, B:K.361, B:K.361 GOL.7: 6 residues within 4Å: Chain A: Q.154, Y.199 Chain B: L.184, V.185, H.186, N.187 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.186, B:N.187, A:Y.199

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

NDP.4: 23 residues within 4Å: Chain A: E.33, K.88, A.90, T.91, I.92, T.93, R.98, N.112, L.304, G.305, E.322, H.325, G.326, T.327, V.328, T.329, R.330, H.331, S.342, T.343, N.344, D.391 Ligands: GOL.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.88, A:T.91, A:T.93, A:T.93, A:R.98, A:N.112, A:G.326, A:G.326, A:T.327, A:V.328, A:T.329, A:N.344, A:N.344 Water bridges: A:K.88, A:T.91, A:A.323, A:T.329, A:T.329, A:T.329, A:H.331, A:A.347 Salt bridges: A:R.330, A:H.331 pi-Stacking: A:H.325 NDP.8: 24 residues within 4Å: Chain B: E.33, K.88, A.90, T.91, I.92, T.93, R.98, N.112, L.304, G.305, E.322, A.324, H.325, G.326, T.327, V.328, T.329, R.330, H.331, S.342, T.343, N.344, D.391 Ligands: CIT.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.88, B:T.91, B:T.91, B:T.93, B:T.93, B:R.98, B:N.112, B:E.322, B:G.326, B:G.326, B:T.327, B:V.328, B:N.344, B:N.344 Water bridges: B:T.329, B:T.329, B:A.347 Salt bridges: B:R.330, B:H.331

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 5 residues within 4Å: Chain B: T.93, S.110, N.112, R.116 Ligands: NDP.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.93, B:S.110 Salt bridges: B:R.116

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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