SMTL ID : 8vhe.1 (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: 27 residues within 4Å: Chain A: 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 Chain B: D.268 Ligands: GOL.4, CA.6 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.91, A:T.93, A:T.93, A:R.98, A:R.98, A:S.110, A:N.112, A:A.324, A:G.326, A:T.327, A:V.328, A:T.329, A:N.344, A:N.344 Water bridges: A:G.113, A:R.116, A:R.116, A:R.125, A:R.125, A:R.125, A:E.322 Salt bridges: A:R.116, A:R.125, A:R.330, A:H.331 01.7: 29 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: GOL.11, CA.13 31 PLIP interactions: 28 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: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:N.344, B:N.344, A:D.268 Water bridges: B:N.112, B:R.116, B:R.116, B:R.125, B:R.125, B:T.329, B:R.330, A:K.228, A:T.230 Salt bridges: B:R.116, B:R.125, B:R.330, B:H.331

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.117, I.118, Y.151, Q.201, S.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.118, A:Q.201, A:S.204 Water bridges: A:S.204 GOL.3: 5 residues within 4Å: Chain A: K.81, L.119, C.313, P.314, D.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.119, A:D.315, A:D.315 GOL.4: 8 residues within 4Å: Chain A: R.125, D.291, S.294, D.295, M.307, A.324 Ligands: 01.1, CA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.291, A:D.291, A:S.294 Water bridges: A:R.125 GOL.8: 5 residues within 4Å: Chain B: N.117, I.118, G.120, Q.201, S.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.118 GOL.10: 3 residues within 4Å: Chain B: W.261, E.263, R.265 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.265 GOL.11: 8 residues within 4Å: Chain B: R.125, D.291, S.294, D.295, M.307, A.324 Ligands: 01.7, CA.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.294, B:D.295 Water bridges: B:R.125

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

CL.5: 4 residues within 4Å: Chain A: E.340, T.341, N.409, F.411 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: E.340, T.341, N.409, T.410, F.411 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.291, D.295 Chain B: D.268 Ligands: 01.1, GOL.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.291, A:D.291, A:D.295, B:D.268 CA.13: 5 residues within 4Å: Chain A: D.268 Chain B: D.291, D.295 Ligands: 01.7, GOL.11 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

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

SCN.9: 5 residues within 4Å: Chain B: K.81, L.119, C.313, P.314, D.315 1 PLIP interactions: 1 interactions with chain B Water bridges: 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 drive distinct kinetic features and possible resistance mechanisms. To Be Published

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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