SMTL ID : 2y41.1

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM and MN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

IPM.1: 11 residues within 4Å: Chain A: E.90, L.94, R.97, R.107, R.135, Y.142, D.244 Chain B: K.188, V.191, D.220 Ligands: MN.2 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.191, A:E.90, A:L.94 Hydrogen bonds: B:K.188 Water bridges: B:N.190 Salt bridges: B:K.188, B:K.188, A:R.97, A:R.97, A:R.107, A:R.135, A:R.135 IPM.3: 10 residues within 4Å: Chain A: K.188, V.191, D.220 Chain B: E.90, R.97, R.107, R.135, Y.142, D.244 Ligands: MN.4 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.90, A:V.191 Salt bridges: B:R.97, B:R.97, B:R.107, B:R.135, B:R.135, A:K.188 Hydrogen bonds: A:K.188

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 5 residues within 4Å: Chain A: D.244, D.248 Chain B: K.188, D.220 Ligands: IPM.1 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.220, A:D.244, H2O.5, H2O.5 MN.4: 5 residues within 4Å: Chain A: K.188, D.220 Chain B: D.244, D.248 Ligands: IPM.3 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.220, B:D.244, H2O.8, H2O.8 MN.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graczer, E. et al., Atomic Level Description of the Domain Closure in a Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase. Mol.Biosyst. (2011)

Release Date

2011-01-19

Peptides

3-ISOPROPYLMALATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-ISOPROPYLMALATE DEHYDROGENASE

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