SMTL ID : 6ajc.2 (3 other biounits)

Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate and ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 23 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.287, A.306, A.307, H.308, G.309, T.310, V.311, T.312, R.313, H.314, T.326, N.327 Chain B: L.249, D.252, K.259 Ligands: ICT.3 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.75, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:A.307, A:G.309, A:T.310, A:V.311, A:T.312, A:R.313, A:N.327, A:N.327, B:D.252 Salt bridges: A:H.314, B:K.259 pi-Stacking: A:H.308 NAP.4: 24 residues within 4Å: Chain A: T.213, L.249, D.252, K.259 Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.287, A.306, A.307, H.308, G.309, T.310, V.311, T.312, R.313, H.314, T.326, N.327 Ligands: ICT.6 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:A.307, B:G.309, B:T.310, B:V.311, B:T.312, B:R.313, B:N.327, B:N.327 Water bridges: B:A.330 Salt bridges: B:H.314, A:K.259

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: R.109, D.274, D.278 Chain B: D.251 Ligands: ICT.3 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.251, A:D.274, A:D.274, A:D.278 CA.5: 5 residues within 4Å: Chain A: D.251 Chain B: R.109, D.274, D.278 Ligands: ICT.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.274, B:D.274, B:D.278, A:D.251

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.3: 14 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.274, A.307 Chain B: K.211, I.214, D.251 Ligands: NAP.1, CA.2 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.77, A:S.94, A:N.96, B:K.211, B:D.251 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.211, B:K.211 ICT.6: 12 residues within 4Å: Chain A: K.211, I.214 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.274 Ligands: NAP.4, CA.5 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:S.94, B:N.96, A:K.211, A:D.251 Salt bridges: B:R.100, B:R.100, B:R.109, B:R.132, B:R.132, A:K.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+). To Be Published

Release Date

2019-08-28

Peptides

Isocitrate dehydrogenase [NADP]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isocitrate dehydrogenase [NADP]

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