SMTL ID : 8vha.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 2.28 Å

Oligo State

homo-dimer

Ligands

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)

EE1.1: 23 residues within 4Å: Chain A: E.33, K.88, A.90, T.91, I.92, T.93, R.98, S.110, N.112, G.305, E.322, A.323, H.325, G.326, T.327, V.328, T.329, R.330, H.331, S.342, T.343, N.344, D.391 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.88, A:T.91, A:T.93, A:T.93, A:R.98, A:S.110, A:N.112, A:N.112, A:G.326, A:G.326, A:T.327, A:V.328, A:N.344, A:N.344 Water bridges: A:A.347 Salt bridges: A:R.330, A:H.331, B:K.228 pi-Stacking: A:H.325

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 7 residues within 4Å: Chain A: V.271, M.275, W.283, Q.293, S.296 Chain B: M.275, S.296 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.293, A:S.296, A:S.296 Water bridges: B:S.296, B:S.296 NO3.5: 4 residues within 4Å: Chain B: L.119, C.313, P.314, D.315 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.315

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.291, D.295 Chain B: D.268 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.291, A:D.295, B:D.268, H2O.3, H2O.4 CA.7: 3 residues within 4Å: Chain A: D.268 Chain B: D.291 Ligands: AKG.6 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.6, H2O.6, H2O.6

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

NDP.4: 17 residues within 4Å: Chain B: E.33, 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.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.93, B:R.98, B:H.325, B:G.326, B:T.327, B:V.328, B:T.329, B:N.344, B:N.344 Salt bridges: B:H.331

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

AKG.6: 9 residues within 4Å: Chain B: T.93, S.110, N.112, R.125, E.322, A.324, H.325 Ligands: NDP.4, CA.7 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.93, B:S.110, B:D.291 Water bridges: B:N.112, B:R.116, B:R.125, A:K.228 Salt bridges: B:R.116, B:R.125, 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

Related Entries With Identical Sequence