SMTL ID : 3vmk.1

3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

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

IPM.1: 10 residues within 4Å: Chain A: E.100, R.108, R.147, Y.154, D.260 Chain B: K.204, N.206, V.207, D.236 Ligands: MG.2 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.207, A:E.100 Hydrogen bonds: B:K.204, B:D.236, B:D.236, A:R.118 Salt bridges: B:K.204, A:R.108, A:R.108, A:R.147, A:R.147 Water bridges: A:R.108, A:R.108, A:R.147, A:S.263 IPM.4: 11 residues within 4Å: Chain A: K.204, N.206, V.207, D.236 Chain B: E.100, R.108, R.118, R.147, Y.154, D.260 Ligands: MG.5 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.100, A:V.207 Hydrogen bonds: B:Y.154, A:K.204 Water bridges: B:R.108, B:R.108, B:R.118, B:R.118, B:R.118, B:R.147 Salt bridges: B:R.108, B:R.108, B:R.118, B:R.147, B:R.147, A:K.204

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.260 Chain B: K.204, D.236 Ligands: IPM.1 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.260, B:D.236, H2O.7, H2O.24 MG.5: 4 residues within 4Å: Chain A: K.204, D.236 Chain B: D.260 Ligands: IPM.4 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.236, B:D.260, H2O.2, H2O.15

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: G.152, I.153, M.174, N.256, L.257 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: G.152, I.153, M.174, N.256, L.257 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagae, T. et al., Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1. Acta Crystallogr.,Sect.F (2012)

Release Date

2012-02-29

Peptides

3-isopropylmalate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-isopropylmalate dehydrogenase