SMTL ID : 1lwd.1

CRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM PORCINE HEART MITOCHONDRIA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: D.275 Chain B: D.252 Ligands: ICT.2 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.1, H2O.1 MN.3: 3 residues within 4Å: Chain A: D.252 Chain B: D.275 Ligands: ICT.6 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.12, H2O.12

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 12 residues within 4Å: Chain A: T.78, S.95, N.97, R.101, R.110, R.133, Y.140, D.275 Chain B: K.212, I.215, D.252 Ligands: MN.1 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:K.212, A:N.97, A:Y.140 Salt bridges: B:K.212, A:R.101, A:R.101, A:R.110, A:R.133, A:R.133 Water bridges: A:T.78, A:R.101 ICT.6: 11 residues within 4Å: Chain A: K.212, D.252 Chain B: T.78, S.95, N.97, R.101, R.110, R.133, Y.140, D.275 Ligands: MN.3 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:K.212, B:T.78, B:N.97 Salt bridges: A:K.212, B:R.101, B:R.101, B:R.110, B:R.133, B:R.133 Water bridges: B:R.110

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain B: H.315, K.374 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.315, B:S.326 Salt bridges: B:H.315, B:K.374 SO4.5: 1 residues within 4Å: Chain B: R.149 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ceccarelli, C. et al., Crystal Structure of Porcine Mitochondrial NADP+-Dependent Isocitrate Dehydrogenase Complexed with Mn2+ and Isocitrate. J.Biol.Chem. (2002)

Release Date

2002-11-13

Peptides

Isocitrate Dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate Dehydrogenase