SMTL ID : 8vhb.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 10 residues within 4Å: Chain A: T.93, S.110, N.112, R.125, D.291, A.324, H.325 Chain B: D.268 Ligands: NDP.2, CA.10 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.93, A:S.110, A:N.112, A:H.325 Water bridges: A:N.112, A:R.116, A:R.125, A:D.291, A:D.295, A:D.295, B:D.268, B:D.268, B:D.268 Salt bridges: A:R.125, A:H.325

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

NDP.2: 16 residues within 4Å: Chain A: 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 Ligands: AKG.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.93, A:T.93, A:R.98, A:H.325, A:T.327, A:V.328, A:T.329, A:R.330, A:N.344, A:N.344 Water bridges: A:G.326 Salt bridges: A:R.330, A:H.331

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.81, L.119, C.313, P.314, D.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.315, A:D.315 GOL.4: 2 residues within 4Å: Chain A: H.210, Q.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Water bridges: A:S.211 GOL.14: 9 residues within 4Å: Chain A: M.275, S.296 Chain B: W.140, V.271, M.275, W.283, Q.293, S.296, V.297 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.271, B:M.275, B:Q.293, B:S.296, B:S.296 Water bridges: A:S.296, A:S.296 GOL.15: 5 residues within 4Å: Chain B: K.81, L.119, C.313, P.314, D.315 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.119, B:D.315 Water bridges: B:T.318 GOL.20: 2 residues within 4Å: Chain B: W.261, E.263 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.263

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

SCN.5: 3 residues within 4Å: Chain A: E.126, I.145, K.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.219 Water bridges: A:R.354 SCN.6: 2 residues within 4Å: Chain A: K.259, I.260 No protein-ligand interaction detected (PLIP) SCN.7: 3 residues within 4Å: Chain A: V.51, E.52, L.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.53 SCN.8: 3 residues within 4Å: Chain A: D.202 Chain B: G.191, G.192 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.203 SCN.13: 4 residues within 4Å: Chain A: V.161 Chain B: K.234, R.238, D.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.234 SCN.16: 5 residues within 4Å: Chain B: A.360, N.364, N.365, K.366, A.369 No protein-ligand interaction detected (PLIP) SCN.17: 5 residues within 4Å: Chain B: D.248, K.249, Q.250, K.252, S.253 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.253 SCN.18: 2 residues within 4Å: Chain B: G.139, K.276 No protein-ligand interaction detected (PLIP) SCN.19: 5 residues within 4Å: Chain A: I.231 Chain B: Q.154, Y.155, R.156, A.157 No protein-ligand interaction detected (PLIP) SCN.21: 4 residues within 4Å: Chain A: P.163, P.165 Chain B: Y.172, P.174 No protein-ligand interaction detected (PLIP)

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

CL.9: 4 residues within 4Å: Chain A: T.341, N.409, T.410, F.411 Ligand excluded by PLIP CL.22: 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.10: 3 residues within 4Å: Chain A: D.291 Chain B: D.268 Ligands: AKG.1 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.268, A:D.291, H2O.2, H2O.4, H2O.5 CA.11: 4 residues within 4Å: Chain A: D.268 Chain B: D.291, D.295 Ligands: EE1.12 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.12, H2O.18, H2O.19

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)

EE1.12: 20 residues within 4Å: Chain A: K.228, D.268 Chain B: T.91, I.92, T.93, R.98, S.110, N.112, D.291, H.325, G.326, T.327, V.328, T.329, R.330, H.331, S.342, T.343, N.344 Ligands: CA.11 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.93, B:T.93, B:R.98, B:R.98, B:S.110, B:N.112, B:T.327, B:V.328, B:T.329, B:N.344, B:N.344 Water bridges: B:G.113, B:G.326, B:T.329, B:T.329, B:H.331, B:H.331, A:D.269 Salt bridges: B:R.330, B:H.331, A:K.228

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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