SMTL ID : 8w49.1 (1 other biounit)

mouse isocitrate dehydrogenase with isocitrate and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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: ICT.4 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:K.72, A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:N.96, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328, B:D.253, B:Q.257, B:Q.257 Water bridges: A:T.77, A:R.314, A:A.331, B:R.249, B:D.253, B:D.253 Salt bridges: A:H.315, B:K.260 NAP.7: 24 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, A.307, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328 Ligands: ICT.8 27 PLIP interactions: 10 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:D.253, A:Q.257, A:Q.257, B:T.75, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:N.96, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328 Water bridges: A:D.253, A:D.253, A:D.253, A:D.253, A:K.260, A:K.260, B:R.100, B:T.313, B:A.331 Salt bridges: A:K.260, B:H.315

2 x MG: MAGNESIUM ION

MG.2: 4 residues within 4Å: Chain A: K.212, D.252 Chain B: D.275 Ligands: ICT.8 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.275, A:D.252, H2O.19, H2O.21 MG.3: 3 residues within 4Å: Chain A: D.275 Chain B: D.252 Ligands: ICT.4 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.275, B:D.252, H2O.3, H2O.4

2 x ICT: ISOCITRIC ACID

ICT.4: 14 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, I.215, D.252 Ligands: NAP.1, MG.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.77, A:S.94, A:N.96, A:D.275, B:K.212 Water bridges: A:R.100, A:R.109, A:R.109, B:T.214 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.212 ICT.8: 14 residues within 4Å: Chain A: K.212, 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: MG.2, NAP.7 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:D.275, B:A.308, A:K.212 Water bridges: B:R.100, B:R.100, B:R.109 Salt bridges: B:R.100, B:R.100, B:R.109, B:R.132, B:R.132, A:K.212

4 x IPA: ISOPROPYL ALCOHOL

IPA.5: 3 residues within 4Å: Chain A: Y.208, Q.257, F.265 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.208, A:Q.257, A:F.265 Water bridges: A:Y.208, A:Y.208 IPA.6: 9 residues within 4Å: Chain A: W.124, V.255, M.259, W.267, Q.277, S.280, V.281 Chain B: M.259, S.280 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.124, A:V.255 Hydrogen bonds: A:Q.277, A:S.280 Water bridges: B:S.280 IPA.9: 5 residues within 4Å: Chain B: Y.208, R.249, M.254, Q.257, F.265 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.208, B:Q.257 IPA.10: 8 residues within 4Å: Chain A: M.259, S.280 Chain B: W.124, V.255, M.259, W.267, Q.277, S.280 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.255, B:M.259, B:W.267 Water bridges: A:S.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, B.S. et al., mouse isocitrate dehydrogenase with isocitrate and magnesium. 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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