SMTL ID : 5j33.3 (3 other biounits)

Isopropylmalate dehydrogenase in complex with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.49 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 23 residues within 4Å: Chain A: A.113, I.114, E.129, L.132, I.301, E.318, P.319, H.321, G.322, S.323, A.324, P.325, D.326, I.327, A.333, N.334, D.375 Chain B: N.234, Y.262, D.264, N.265, M.268 Ligands: SO4.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.114, A:D.120, A:E.129, A:E.318, A:G.322, A:G.322, A:S.323, A:A.324, A:D.326, A:N.334, A:N.334, B:N.234, B:N.265 NAD.3: 26 residues within 4Å: Chain A: Y.262, D.264, N.265, M.268 Chain B: I.53, I.114, G.115, G.116, D.120, E.129, L.132, R.136, G.302, E.318, H.321, G.322, S.323, A.324, P.325, D.326, I.327, A.333, N.334, D.375 Ligands: SO4.4, MG.5 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.114, B:D.120, B:E.129, B:R.136, B:E.318, B:H.321, B:G.322, B:G.322, B:S.323, B:A.324, B:D.326, B:N.334, B:N.334, A:N.234, A:N.265

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

SO4.2: 6 residues within 4Å: Chain A: R.136, R.146, R.174, D.288 Ligands: NAD.1, MG.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.136, A:R.146, A:R.174, B:K.232 SO4.4: 7 residues within 4Å: Chain A: K.232 Chain B: R.136, R.146, R.174, D.288 Ligands: NAD.3, MG.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.288 Salt bridges: B:R.136, B:R.146, B:R.174, A:K.232

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.264 Chain B: D.288, D.292 Ligands: NAD.3, SO4.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.264, B:D.288, B:D.288 MG.6: 5 residues within 4Å: Chain A: R.146, D.288, D.292 Chain B: D.264 Ligands: SO4.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:D.264, A:D.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S.G. et al., Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS. J.Biol.Chem. (2016)

Release Date

2016-05-18

Peptides

3-isopropylmalate dehydrogenase 2, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

3-isopropylmalate dehydrogenase 2, chloroplastic

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