SMTL ID : 8vhb.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 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.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.93, A:S.110, A:N.112, A:D.291, A:H.325 Water bridges: A:R.116, A:R.125, A:R.125 Salt bridges: A:R.125, A:H.325

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

NDP.2: 17 residues within 4Å: Chain A: T.91, I.92, T.93, P.94, 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 12 PLIP interactions: 12 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:N.344, A:N.344 Water bridges: A:H.331 Salt bridges: A:R.330, A:H.331

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

SCN.3: 8 residues within 4Å: Chain A: M.307, T.308, S.309, V.310, E.322, A.347, F.350, A.351 No protein-ligand interaction detected (PLIP) SCN.4: 6 residues within 4Å: Chain A: R.135, L.136, V.137, S.138 Chain B: L.136, S.138 No protein-ligand interaction detected (PLIP) SCN.9: 3 residues within 4Å: Chain B: Q.244, D.248, K.252 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.244, B:K.252 SCN.12: 4 residues within 4Å: Chain B: M.215, V.310, V.312, R.354 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.354 SCN.14: 4 residues within 4Å: Chain A: K.109 Chain B: T.230, I.231, K.233 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.233

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: W.140, V.271, A.274, M.275, W.283, Q.293, S.296, V.297 Chain B: M.275, S.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.275, A:S.296, A:S.296 GOL.10: 6 residues within 4Å: Chain B: A.127, I.128, I.129, F.350, R.354, E.376 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.129, B:I.129, B:R.354 Water bridges: B:R.354 GOL.11: 8 residues within 4Å: Chain B: D.207, H.210, S.211, Q.214, V.312, C.313, P.314, G.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.211, B:G.316

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

CL.6: 4 residues within 4Å: Chain A: T.341, N.409, T.410, F.411 Ligand excluded by PLIP CL.15: 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.7: 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.4 CA.16: 3 residues within 4Å: Chain A: D.268 Chain B: D.291 Ligands: EE1.8 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.8, H2O.8, H2O.13

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)

EE1.8: 21 residues within 4Å: Chain A: K.228, L.266, 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.16 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.93, B:R.98, B:R.98, B:S.110, B:N.112, B:D.291, B:T.327, B:V.328, B:T.329, B:N.344, B:N.344 Water bridges: B:T.93, B:T.93, B:G.326, B:H.331 Salt bridges: B:R.330, B:H.331, A:K.228

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 9 residues within 4Å: Chain B: N.117, G.120, G.121, H.149, Y.151, Q.201, S.204, D.207, P.314 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.121, B:Q.201 Water bridges: B:Y.151

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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