SMTL ID : 4ajc.1

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, calcium(II) and adenine nucleotide phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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 Chain B: R.292 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.341, A:A.342, A:Y.345, A:Y.345, A:N.352, A:N.352, A:Y.391, B:R.292 Water bridges: A:T.341, A:S.355, A:R.395, A:R.395, B:R.292 Salt bridges: A:K.344 A2P.5: 12 residues within 4Å: Chain A: R.292 Chain B: G.321, H.339, G.340, T.341, A.342, K.344, Y.345, V.351, N.352, Y.391, D.392 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.341, B:A.342, B:Y.345, B:N.352, B:N.352, B:Y.391, A:R.292 Water bridges: B:T.341, B:S.355, B:R.395, B:R.395, A:R.292 Salt bridges: B:K.344

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

AKG.2: 11 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 Ligands: CA.3 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.160, B:I.233 Hydrogen bonds: A:S.113, A:R.119, A:Y.160, B:N.232 Water bridges: A:R.119, A:R.119, A:R.129, A:R.129, A:R.129, A:R.129, A:D.311, A:E.336 Salt bridges: A:R.119, A:R.129, A:R.153 AKG.6: 11 residues within 4Å: Chain A: K.230, N.232, I.233 Chain B: S.113, N.115, R.119, R.129, R.153, Y.160, D.307 Ligands: CA.7 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.160, A:I.233 Hydrogen bonds: B:S.113, B:R.119, A:N.232 Water bridges: B:T.105, B:R.119, B:R.119, B:R.129, B:R.129, B:R.129, B:R.129, B:D.311, B:E.336 Salt bridges: B:R.119, B:R.129, B:R.153

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.307, D.311 Chain B: D.283 Ligands: AKG.2 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.283, A:D.307, A:D.311, H2O.14, H2O.17 CA.7: 4 residues within 4Å: Chain A: D.283 Chain B: D.307, D.311 Ligands: AKG.6 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.307, B:D.311, A:D.283, H2O.30, H2O.33

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

SO4.4: 6 residues within 4Å: Chain A: V.107, G.108, G.109, G.110, I.111 Chain B: K.235 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.108, A:G.110, A:I.111 Water bridges: A:G.109, A:I.111, B:K.235 Salt bridges: B:K.235 SO4.8: 6 residues within 4Å: Chain A: K.235 Chain B: V.107, G.108, G.109, G.110, I.111 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.108, B:G.110, B:I.111 Water bridges: B:G.109, 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

NADP ISOCITRATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NADP ISOCITRATE DEHYDROGENASE

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