SMTL ID : 5hn6.1

Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and 3-isopropylmalate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

IPM.1: 9 residues within 4Å: Chain A: L.83, R.86, R.96, R.111, Y.118, D.218 Chain B: K.163, D.194 Ligands: MN.2 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:K.163, A:Y.118 Salt bridges: B:K.163, A:R.86, A:R.86, A:R.96, A:R.111, A:R.111 Hydrophobic interactions: A:L.83 Water bridges: A:R.96 IPM.4: 9 residues within 4Å: Chain A: K.163, D.194 Chain B: L.83, R.86, R.96, R.111, Y.118, D.218 Ligands: MN.5 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.83 Water bridges: B:R.96 Salt bridges: B:R.86, B:R.86, B:R.96, B:R.111, B:R.111, A:K.163 Hydrogen bonds: A:K.163

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.218, D.222 Chain B: K.163, D.194 Ligands: IPM.1 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.194, A:D.218, H2O.1, H2O.1 MN.5: 5 residues within 4Å: Chain A: K.163, D.194 Chain B: D.218, D.222 Ligands: IPM.4 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.218, A:D.194, H2O.1, H2O.2

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 8 residues within 4Å: Chain A: I.12, S.230, H.250, A.253, I.256, A.262, N.263, D.301 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.12, A:A.253, A:D.301 Hydrogen bonds: A:N.263 MPD.6: 8 residues within 4Å: Chain B: I.12, S.230, H.250, A.253, I.256, A.262, N.263, D.301 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.12, B:A.253, B:D.301 Hydrogen bonds: B:N.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, T. et al., Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis. Biochem. J. (2017)

Release Date

2016-12-07

Peptides

Homoisocitrate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Homoisocitrate dehydrogenase

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