SMTL ID : 4ajs.1

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x A2P: ADENOSINE-2'-5'-DIPHOSPHATE(Non-covalent)

A2P.1: 12 residues within 4Å: Chain A: G.321, H.339, G.340, T.341, A.342, K.344, Y.345, V.351, N.352, Y.391, D.392, R.395 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.342, A:Y.345, A:Y.345, A:Y.345, A:N.352, A:N.352, A:Y.391 Water bridges: A:G.340, A:G.340, A:T.341, A:T.341 Salt bridges: A:K.344, A:R.395 A2P.6: 12 residues within 4Å: Chain B: G.321, H.339, G.340, T.341, A.342, K.344, Y.345, V.351, N.352, Y.391, D.392, R.395 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.342, B:Y.345, B:Y.345, B:N.352, B:N.352, B:Y.391 Water bridges: B:G.340, B:G.340, B:T.341, B:T.341, B:D.392, B:D.392 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, N.115, R.119, R.129, R.153, Y.160, D.307 Chain B: K.230, N.232, I.233, D.283 Ligands: MG.3 12 PLIP interactions: 9 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: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.7: 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.8 11 PLIP interactions: 8 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: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: 4 residues within 4Å: Chain A: D.307 Chain B: K.230, D.283 Ligands: ICT.2 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.8, H2O.16 MG.8: 4 residues within 4Å: Chain A: K.230, D.283 Chain B: D.307 Ligands: ICT.7 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.28, H2O.36

2 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.4: 5 residues within 4Å: Chain A: K.344 Chain B: I.258, G.261, P.262, W.263 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.258, B:W.263 pi-Stacking: B:W.263, B:W.263 Salt bridges: A:K.344 NMN.9: 5 residues within 4Å: Chain A: I.258, G.261, P.262, W.263 Chain B: K.344 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:K.344 Hydrogen bonds: A:I.258, A:W.263 pi-Stacking: A:W.263, A:W.263

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

SO4.5: 5 residues within 4Å: Chain A: V.107, G.108, G.109, G.110 Chain B: K.235 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.108, A:G.110 Water bridges: A:P.106, A:I.111, B:K.235 Salt bridges: B:K.235 SO4.10: 5 residues within 4Å: Chain A: K.235 Chain B: V.107, G.108, G.109, G.110 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.108, B:G.110 Water bridges: B:P.106, B:I.111, A:K.235 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

ISOCITRATE DEHYDROGENASE [NADP]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ISOCITRATE DEHYDROGENASE [NADP]

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