SMTL ID : 4ajb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x TAP: 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

TAP.1: 18 residues within 4Å: Chain A: I.37, L.103, T.104, T.105, T.338, H.339, G.340, T.341, A.342, K.344, Y.345, V.351, N.352, Y.391, D.392, R.395 Chain B: R.292 Ligands: ICT.2 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.105, A:T.105, A:T.338, A:A.342, A:Y.345, A:N.352, A:N.352, A:Y.391, A:Y.391, B:R.292 Water bridges: A:L.103, A:L.103, A:T.105, A:N.115, A:R.129, A:T.338, A:G.340, A:G.340, A:T.341, A:T.341 Salt bridges: A:K.344, A:R.395 TAP.5: 18 residues within 4Å: Chain A: R.292 Chain B: I.37, L.103, T.104, T.105, T.338, H.339, G.340, T.341, A.342, K.344, Y.345, V.351, N.352, Y.391, D.392, R.395 Ligands: ICT.6 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.105, B:T.105, B:T.338, B:A.342, B:N.352, B:N.352, B:Y.391, B:Y.391, A:R.292 Water bridges: B:L.103, B:L.103, B:N.115, B:R.129, B:T.338, B:G.340, B:G.340, B:T.341, B:T.341, B:T.341 Salt bridges: B:K.344, B:R.395

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.2: 12 residues within 4Å: Chain A: S.113, R.119, R.129, R.153, Y.160, D.307 Chain B: K.230, N.232, I.233, D.283 Ligands: TAP.1, MG.3 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.113, A:Y.160, B:K.230, B:N.232 Water bridges: A:T.105, A:R.129, A:R.129, A:D.311 Salt bridges: A:R.119, A:R.119, A:R.129, A:R.153, A:R.153, B:K.230 ICT.6: 12 residues within 4Å: Chain A: K.230, N.232, I.233, D.283 Chain B: S.113, R.119, R.129, R.153, Y.160, D.307 Ligands: TAP.5, MG.7 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.113, A:K.230, A:N.232 Water bridges: B:R.129, B:R.129, B:D.311 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.3: 5 residues within 4Å: Chain A: D.307, D.311 Chain B: K.230, D.283 Ligands: ICT.2 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.283, A:D.307, H2O.8, H2O.16 MG.7: 5 residues within 4Å: Chain A: K.230, D.283 Chain B: D.307, D.311 Ligands: ICT.6 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.27, H2O.34

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

SO4.4: 5 residues within 4Å: Chain A: V.107, G.108, G.109, G.110 Chain B: K.235 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.108, A:G.109, A:G.110 Water bridges: A:I.111, A:I.111 Salt bridges: B:K.235 SO4.8: 5 residues within 4Å: Chain A: K.235 Chain B: V.107, G.108, G.109, G.110 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.108, B:G.109, B:G.110 Water bridges: B:I.111, B:I.111 Salt bridges: A:K.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goncalves, S. et al., Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase. Biochemistry (2012)

Release Date

2012-10-31

Peptides

NADP ISOCITRATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADP ISOCITRATE DEHYDROGENASE

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