SMTL ID : 4bnp.1

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.1: 12 residues within 4Å: Chain A: S.113, N.115, R.119, R.129, R.153, Y.160, D.307 Chain B: K.230, N.232, I.233, D.283 Ligands: MG.2 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.113, A:S.113, B:K.230, B:N.232, B:D.283 Water bridges: A:R.129, A:R.129, A:R.129 Salt bridges: A:R.119, A:R.119, A:R.129, A:R.153, A:R.153, B:K.230 ICT.4: 12 residues within 4Å: Chain A: K.230, N.232, I.233, D.283 Chain B: S.113, N.115, R.119, R.129, R.153, Y.160, D.307 Ligands: MG.5 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.113, B:S.113, B:Y.160, A:K.230, A:N.232, A:D.283 Water bridges: B:R.129, B:R.129, B:R.129 Salt bridges: B:R.119, B:R.119, B:R.129, B:R.153, B:R.153, A:K.230

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.307, D.311 Chain B: K.230, D.283 Ligands: ICT.1 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.307, B:D.283, H2O.9, H2O.17 MG.5: 5 residues within 4Å: Chain A: K.230, D.283 Chain B: D.307, D.311 Ligands: ICT.4 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.307, A:D.283, H2O.30, H2O.38

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

SO4.3: 6 residues within 4Å: Chain A: V.107, G.108, G.109, G.110, I.111 Chain B: K.235 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.108, A:G.110, A:I.111 Water bridges: A:P.106, A:G.109, A:G.109, B:K.235 Salt bridges: B:K.235 SO4.6: 6 residues within 4Å: Chain A: K.235 Chain B: V.107, G.108, G.109, G.110, I.111 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.108, B:G.110, B:I.111 Water bridges: B:P.106, B:G.109, B:G.109, A:K.235 Salt bridges: A:K.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, S.P. et al., Evolution of a Transition State: Role of Lys100 in the Active Site of Isocitrate Dehydrogenase. Chembiochem (2014)

Release Date

2014-05-21

Peptides

ISOCITRATE DEHYDROGENASE [NADP]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ISOCITRATE DEHYDROGENASE [NADP]

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