SMTL ID : 1hj6.1

ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: L.16, R.96, I.328, G.329, D.330, C.332, A.333, H.366 Ligands: GOL.2 No protein-ligand interaction detected (PLIP) GOL.2: 5 residues within 4Å: Chain A: F.152, Y.216, I.328, H.366 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.366 GOL.6: 9 residues within 4Å: Chain B: L.16, R.96, I.328, G.329, D.330, C.332, A.333, H.366 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) GOL.7: 5 residues within 4Å: Chain B: F.152, Y.216, I.328, H.366 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.366

2 x IPM: 3-ISOPROPYLMALIC ACID(Non-covalent)

IPM.3: 13 residues within 4Å: Chain A: E.113, V.116, R.119, R.129, R.153, Y.160, D.307 Chain B: K.230, N.232, I.233, D.283 Ligands: NAP.4, MG.5 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.113, A:V.116, B:I.233 Hydrogen bonds: A:Y.160, B:K.230, B:D.283 Water bridges: A:R.119, A:R.129, B:D.283 Salt bridges: A:R.119, A:R.119, A:R.129, A:R.153, A:R.153, B:K.230 IPM.8: 13 residues within 4Å: Chain A: K.230, N.232, I.233, D.283 Chain B: E.113, V.116, R.119, R.129, R.153, Y.160, D.307 Ligands: NAP.9, MG.10 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:I.233, B:E.113, B:V.116 Hydrogen bonds: A:K.230, A:D.283 Water bridges: A:D.283, A:D.283, A:D.283, B:R.119, B:R.129 Salt bridges: A:K.230, B:R.119, B:R.119, B:R.129, B:R.153, B:R.153

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

NAP.4: 25 residues within 4Å: Chain A: I.37, K.100, P.102, L.103, T.104, N.115, R.119, I.320, G.321, E.336, T.338, H.339, G.340, T.341, A.342, Y.345, V.351, N.352, Y.391, D.392 Chain B: N.232, I.281, Q.288, R.292 Ligands: IPM.3 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.100, A:L.103, A:T.104, A:N.115, A:R.119, A:E.336, A:G.340, A:G.340, A:T.341, A:A.342, A:Y.345, A:N.352, A:N.352, A:Y.391, B:N.232 Water bridges: A:T.105, A:G.321, A:E.336, A:E.336, B:Q.287, B:Q.288, B:R.292, B:R.292 Salt bridges: B:R.292 NAP.9: 25 residues within 4Å: Chain A: N.232, I.281, Q.288, R.292 Chain B: I.37, K.100, P.102, L.103, T.104, N.115, R.119, I.320, G.321, E.336, T.338, H.339, G.340, T.341, A.342, Y.345, V.351, N.352, Y.391, D.392 Ligands: IPM.8 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.100, B:L.103, B:N.115, B:R.119, B:E.336, B:G.340, B:G.340, B:T.341, B:A.342, B:N.352, B:N.352, B:Y.391, A:N.232 Water bridges: B:T.105, B:G.321, A:Q.287, A:Q.288, A:R.292, A:R.292 Salt bridges: A:R.292

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.307, D.311 Chain B: D.283 Ligands: IPM.3 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.187, H2O.201 MG.10: 4 residues within 4Å: Chain A: D.283 Chain B: D.307, D.311 Ligands: IPM.8 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.419, H2O.433

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doyle, S.A. et al., Structural Basis for a Change in Substrate Specificity: Crystal Structure of S113E Isocitrate Dehydrogenase in a Complex with Isopropylmalate, Mg2+ and Nadp. Biochemistry (2001)

Release Date

2001-01-16

Peptides

ISOCITRATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ISOCITRATE DEHYDROGENASE

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