SMTL ID : 4ajr.1

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, magnesium(II) and NADPH - The product complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

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

NMN.1: 6 residues within 4Å: Chain A: K.344 Chain B: I.258, D.259, 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, A:K.344 pi-Stacking: B:W.263, B:W.263 NMN.5: 6 residues within 4Å: Chain A: I.258, D.259, G.261, P.262, W.263 Chain B: K.344 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.258, A:W.263, B:K.344 pi-Stacking: A:W.263, A:W.263

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 30 residues within 4Å: Chain A: I.37, P.102, L.103, T.104, T.105, N.115, R.119, I.320, G.321, E.336, T.338, H.339, G.340, T.341, A.342, P.343, K.344, Y.345, V.351, N.352, Y.391, D.392 Chain B: N.232, I.281, A.284, Q.287, Q.288, R.292 Ligands: AKG.3, MG.4 25 PLIP interactions: 20 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:L.103, A:T.105, A:T.105, A:N.115, A:R.119, A:E.336, A:G.340, A:G.340, A:T.341, A:A.342, A:K.344, A:Y.345, A:N.352, A:N.352, A:Y.391, A:Y.391, B:N.232, B:Q.287, B:Q.288, B:Q.288 Water bridges: A:I.320, A:E.336, A:E.336 Salt bridges: A:K.344, B:R.292 NAP.6: 30 residues within 4Å: Chain A: N.232, I.281, A.284, Q.287, Q.288, R.292 Chain B: I.37, P.102, L.103, T.104, T.105, N.115, R.119, I.320, G.321, E.336, T.338, H.339, G.340, T.341, A.342, P.343, K.344, Y.345, V.351, N.352, Y.391, D.392 Ligands: AKG.7, MG.8 23 PLIP interactions: 5 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:N.232, A:Q.287, A:Q.288, A:Q.288, B:L.103, B:T.105, B:T.105, B:T.105, B:N.115, B:R.119, B:E.336, B:G.340, B:G.340, B:T.341, B:A.342, B:K.344, B:N.352, B:N.352, B:Y.391, B:Y.391 Salt bridges: A:R.292, B:K.344 Water bridges: B:I.320

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 16 residues within 4Å: Chain A: L.103, T.105, S.113, N.115, R.119, R.129, R.153, Y.160, D.307, T.338 Chain B: K.230, N.232, I.233, D.283 Ligands: NAP.2, MG.4 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.105, A:T.105, A:S.113, A:N.115, A:Y.160, A:T.338, B:K.230, B:N.232 Water bridges: A:R.119, A:R.129 Salt bridges: A:R.119, A:R.129, A:R.153 AKG.7: 16 residues within 4Å: Chain A: K.230, N.232, I.233, D.283 Chain B: L.103, T.105, S.113, N.115, R.119, R.129, R.153, Y.160, D.307, T.338 Ligands: NAP.6, MG.8 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.105, B:S.113, B:N.115, B:T.338, A:K.230, A:N.232 Water bridges: B:R.119, B:R.129 Salt bridges: B:R.119, B:R.129, B:R.153

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.307, D.311 Chain B: D.283 Ligands: NAP.2, AKG.3 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.2, H2O.5 MG.8: 5 residues within 4Å: Chain A: D.283 Chain B: D.307, D.311 Ligands: NAP.6, AKG.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.7, H2O.9

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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