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

Crystal Structure of Human IDH1 R132Q in Complex with NADPH-TCEP Adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x 01: 3,3',3''-({(4R)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1,4-dihydropyridin-4-yl}-lambda~5~-phosphanetriyl)tripropanoic acid

01.1: 31 residues within 4Å: Chain A: K.88, A.90, T.91, I.92, T.93, R.98, S.110, N.112, R.116, R.125, D.291, D.295, L.304, G.305, S.309, E.322, 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: D.268 Ligands: GOL.2, CA.5 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.91, A:T.93, A:R.98, A:R.98, A:S.110, A:N.112, A:E.322, A:G.326, A:T.327, A:V.328, A:N.344, A:N.344 Water bridges: A:R.116, A:R.125, A:D.295, A:S.309, A:S.309, A:T.329, A:T.329, A:H.331, A:A.347, B:K.228, B:K.228 Salt bridges: A:R.116, A:R.125, A:R.330, A:H.331, B:K.228 pi-Stacking: A:H.325 01.7: 30 residues within 4Å: Chain A: I.231, D.268 Chain B: K.88, A.90, T.91, I.92, T.93, R.98, S.110, N.112, R.116, R.125, D.291, D.295, 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 Ligands: SCN.8, GOL.9, CA.11 32 PLIP interactions: 29 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.88, B:T.91, B:T.91, B:T.93, B:T.93, B:R.98, B:R.98, B:S.110, B:N.112, B:A.324, B:G.326, B:T.327, B:V.328, B:T.329, B:R.330, B:N.344, B:N.344 Water bridges: B:T.93, B:R.116, B:R.125, B:R.125, B:R.125, B:H.325, B:H.325, B:R.330, A:K.228, A:K.228 Salt bridges: B:R.116, B:R.125, B:R.330, B:H.331, A:K.228

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: R.125, D.291, S.294, D.295, A.298, M.307, A.324 Ligands: 01.1, CA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.291, A:S.294, A:A.324 GOL.6: 8 residues within 4Å: Chain B: N.117, I.118, L.119, G.120, Y.151, Q.201, S.204, P.314 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.118, B:Q.201 Water bridges: B:L.119 GOL.9: 7 residues within 4Å: Chain B: R.125, D.291, S.294, D.295, A.324 Ligands: 01.7, CA.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.125, B:S.294, B:D.295

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 6 residues within 4Å: Chain A: K.88, N.112, R.116, L.311, E.320, E.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.112 SCN.8: 5 residues within 4Å: Chain B: S.303, L.304, G.305, D.391 Ligands: 01.7 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: T.341, N.409, T.410, F.411 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: T.341, N.409, T.410, F.411 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.291, D.295 Chain B: D.268 Ligands: 01.1, GOL.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.268, A:D.291, A:D.291, A:D.295 CA.11: 5 residues within 4Å: Chain A: D.268 Chain B: D.291, D.295 Ligands: 01.7, GOL.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.291, B:D.291, B:D.295, A:D.268

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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