SMTL ID : 5yfn.1

Human isocitrate dehydrogenase 1 bound with isocitrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: R.116, D.282, D.286 Chain B: D.259 Ligands: ICT.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.259, A:D.282 MG.3: 4 residues within 4Å: Chain A: D.259 Chain B: R.116, D.282 Ligands: ICT.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.259, B:D.282

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 13 residues within 4Å: Chain A: T.84, S.101, N.103, R.107, R.116, R.139, Y.146, D.282, A.315 Chain B: K.219, D.259 Ligands: MG.1, K.6 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.101, A:N.103, A:Y.146, B:K.219, B:K.219 Water bridges: A:T.84, A:R.107, B:K.219 Salt bridges: A:R.107, A:R.107, A:R.116, A:R.139, A:R.139, B:K.219, B:K.219 ICT.5: 14 residues within 4Å: Chain A: K.219, I.222, D.259 Chain B: T.84, S.101, N.103, R.107, R.116, R.139, Y.146, D.282, A.315 Ligands: MG.3, K.4 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.84, B:N.103, A:K.219 Salt bridges: B:R.107, B:R.107, B:R.116, B:R.139, B:R.139, A:K.219, A:K.219

2 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: K.219, D.259, D.260 Ligands: ICT.5 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain B: D.259, D.260 Ligands: ICT.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nordlund, P. et al., Human isocitrate dehydrogenase 1 bound with isocitrate. To Be Published

Release Date

2017-10-25

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic