SMTL ID : 1t0l.2 (1 other biounit)

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: R.109, D.275, D.279 Chain B: D.252 Ligands: ICT.3 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, A:D.275, B:D.252, H2O.1, H2O.6 CA.4: 5 residues within 4Å: Chain A: D.252 Chain B: R.109, D.275, D.279 Ligands: ICT.6 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.275, B:D.275, A:D.252, H2O.12, H2O.13

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 24 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Chain B: D.253, Q.257, K.260 Ligands: ICT.3 25 PLIP interactions: 6 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:Q.257, A:K.72, A:T.75, A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:G.310, A:G.310, A:T.311, A:V.312, A:R.314, A:R.314, A:N.328, A:N.328 Water bridges: B:D.253, B:D.253, B:K.260, B:K.260, A:A.331, A:D.375 Salt bridges: B:K.260, A:H.315 NAP.5: 24 residues within 4Å: Chain A: D.253, Q.257, K.260 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, A.307, A.308, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: ICT.6 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.72, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:G.310, B:G.310, B:T.311, B:V.312, B:R.314, B:N.328, B:N.328 Water bridges: B:T.75, B:H.315, A:D.253 Salt bridges: B:H.315, A:K.260 pi-Stacking: B:H.309

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.3: 15 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275, A.308 Chain B: K.212, T.214, I.215, D.252 Ligands: CA.1, NAP.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.77, A:N.96, B:K.212 Water bridges: A:R.100, A:R.109, A:D.279, A:D.279, A:D.279 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.212, B:K.212 ICT.6: 15 residues within 4Å: Chain A: K.212, T.214, I.215, D.252 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275, A.308 Ligands: CA.4, NAP.5 18 PLIP interactions: 3 interactions with chain A, 15 interactions with chain B Hydrogen bonds: A:K.212, B:T.77, B:S.94, B:S.94, B:S.94 Salt bridges: A:K.212, A:K.212, B:R.100, B:R.100, B:R.109, B:R.132, B:R.132 Water bridges: B:R.100, B:R.100, B:R.109, B:S.278, B:D.279, B:D.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity. J.Biol.Chem. (2004)

Release Date

2004-06-15

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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