SMTL ID : 4aja.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

TAP.1: 19 residues within 4Å: Chain A: I.37, L.103, T.104, T.105, N.115, T.338, H.339, G.340, T.341, A.342, Y.345, V.351, N.352, Y.391, D.392, R.395 Chain B: N.232, I.281 Ligands: ICT.2 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.105, A:T.105, A:N.115, A:T.338, A:A.342, A:Y.345, A:N.352, A:N.352, A:Y.391, A:Y.391 Water bridges: A:L.103, A:L.103, A:L.103, A:R.119, A:H.339, A:G.340, A:G.340, A:T.341, A:T.341, B:N.232 Salt bridges: A:R.395 Hydrophobic interactions: B:I.281 TAP.5: 19 residues within 4Å: Chain A: N.232, I.281 Chain B: I.37, L.103, T.104, T.105, N.115, T.338, H.339, G.340, T.341, A.342, Y.345, V.351, N.352, Y.391, D.392, R.395 Ligands: ICT.6 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.105, B:T.105, B:N.115, B:T.338, B:H.339, B:A.342, B:N.352, B:Y.391, B:Y.391 Water bridges: B:L.103, B:L.103, B:L.103, B:R.119, B:H.339, B:G.340, B:G.340, B:T.341, B:T.341, B:T.341, A:N.232 Salt bridges: B:R.395 Hydrophobic interactions: A:I.281

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, D.283 Ligands: TAP.1, CA.3 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:K.230, B:N.232, A:S.113, A:N.115, A:Y.160 Salt bridges: B:K.230, A:R.119, A:R.119, A:R.129, A:R.153, A:R.153 Water bridges: A:R.129, A:R.129, A:T.338, A:T.338 ICT.6: 12 residues within 4Å: Chain A: K.230, N.232, D.283 Chain B: S.113, N.115, R.119, R.129, R.153, Y.160, D.307 Ligands: TAP.5, CA.7 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.113, B:N.115, A:K.230, A:N.232 Water bridges: B:R.129, B:T.338, B:T.338, A:D.283 Salt bridges: B:R.119, B:R.119, B:R.129, B:R.153, B:R.153, A:K.230

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.307, D.311 Chain B: D.283 Ligands: ICT.2 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.307, A:D.311, B:D.283, H2O.8, H2O.16 CA.7: 4 residues within 4Å: Chain A: D.283 Chain B: D.307, D.311 Ligands: ICT.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.28, H2O.36

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 8 PLIP interactions: 7 interactions with chain A, 1 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, A:I.111 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 8 PLIP interactions: 7 interactions with chain B, 1 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, 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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