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

NADP+-dependent cytosolic isocitrate dehydrogenase complexed with oxaloacetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NAP.1: 23 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Chain B: L.250, D.253, Q.257, K.260 Ligands: OAA.2 32 PLIP interactions: 23 interactions with chain A, 9 interactions with chain B Hydrogen bonds: 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:T.311, A:V.312, A:N.328, A:N.328, B:D.253, B:Q.257 Water bridges: A:T.77, A:N.96, A:E.306, A:T.313, A:R.314, A:R.314, A:H.315, A:A.331, A:D.375, B:D.253, B:D.253, B:Q.257, B:K.260, B:K.260, B:K.260 Salt bridges: A:H.315, B:K.260 NAP.6: 23 residues within 4Å: Chain A: L.250, 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, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: OAA.7 31 PLIP interactions: 23 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:K.72, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328, A:D.253, A:Q.257 Water bridges: B:K.72, B:T.77, B:N.96, B:R.100, B:A.308, B:T.313, B:R.314, B:H.315, B:A.331, B:D.375, A:R.249, A:D.253, A:D.253, A:D.253, A:K.260 Salt bridges: B:H.315, A:K.260

4 x OAA: OXALOACETATE ION

OAA.2: 11 residues within 4Å: Chain A: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275 Chain B: K.212, I.215 Ligands: NAP.1 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.77, A:S.94, A:N.96, B:K.212 Water bridges: A:R.100, A:R.109 Salt bridges: A:R.100, A:R.109, A:R.132, B:K.212, B:K.212 OAA.3: 5 residues within 4Å: Chain A: R.140, Y.183 Chain B: V.169, H.170, D.171 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.183, A:Y.183, B:D.171 Water bridges: A:K.93, A:N.101, A:N.101, A:R.140 Salt bridges: A:R.140, B:H.170 OAA.7: 11 residues within 4Å: Chain A: K.212, I.215 Chain B: T.77, S.94, N.96, R.100, R.109, R.132, Y.139, D.275 Ligands: NAP.6 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, A:K.212 Water bridges: B:R.100 Salt bridges: B:R.100, B:R.109, B:R.132, A:K.212 OAA.8: 6 residues within 4Å: Chain A: M.168, V.169, H.170, D.171 Chain B: R.140, Y.183 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.183, A:D.171 Water bridges: B:N.101, B:R.140, B:R.140, B:R.140, B:R.140, B:T.142, B:Y.183, A:V.169 Salt bridges: B:R.140, A:H.170

4 x IPA: ISOPROPYL ALCOHOL

IPA.4: 3 residues within 4Å: Chain A: Y.208, Q.257, F.265 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.208, A:F.265 Hydrogen bonds: A:Y.208 Water bridges: A:Y.208 IPA.5: 8 residues within 4Å: Chain A: W.124, V.255, M.259, W.267, Q.277, S.280 Chain B: M.259, S.280 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.124, A:W.267 Hydrogen bonds: A:V.255 Water bridges: A:Q.277 IPA.9: 9 residues within 4Å: Chain A: M.259, S.280 Chain B: W.124, V.255, M.259, W.267, Q.277, S.280, V.281 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.124, B:V.255 Hydrogen bonds: B:S.280 Water bridges: B:Q.277 IPA.10: 3 residues within 4Å: Chain B: Y.208, Q.257, F.265 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.208, B:Q.257, B:F.265 Hydrogen bonds: B:Y.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, B.S. et al., NADP+-dependent cytosolic isocitrate dehydrogenase complexed with oxaloacetate. To Be Published

Release Date

2024-09-04

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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