SMTL ID : 6pay.2 (1 other biounit)

Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.1: 13 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: MG.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.94, A:N.96, A:Y.139, B:K.212 Water bridges: A:T.77 Salt bridges: A:R.100, A:R.100, A:R.109, A:R.132, A:R.132, B:K.212 ICT.5: 14 residues within 4Å: Chain A: K.212, I.215, D.252 Chain B: T.77, S.94, N.96, G.97, R.100, R.109, R.132, Y.139, D.275, A.308 Ligands: MG.6 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.77, B:S.94, B:N.96, B:D.275, A:K.212 Salt bridges: B:R.100, B:R.100, B:R.109, B:R.132, B:R.132, A:K.212 Water bridges: A:T.214

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: R.109, R.132, D.275, D.279 Chain B: K.212, D.252 Ligands: ICT.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.252, A:D.275 MG.6: 5 residues within 4Å: Chain A: D.252 Chain B: R.109, D.275, D.279 Ligands: ICT.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.275, A:D.252

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: E.110, A.111, I.112, I.113, F.334, R.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.113, A:R.338 Water bridges: A:A.111, A:R.338 FMT.4: 6 residues within 4Å: Chain A: F.108, E.110, I.129, M.199, K.203, R.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.203 Water bridges: A:F.108, A:E.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roman, J.V. et al., Transient-State Analysis of Human Isocitrate Dehydrogenase I: Accounting for the Interconversion of Active and Non-Active Conformational States. Biochemistry (2019)

Release Date

2019-09-18

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Isocitrate dehydrogenase [NADP] cytoplasmic

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