SMTL ID : 5hn5.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x ICT: ISOCITRIC ACID(Non-covalent)

ICT.1: 11 residues within 4Å: Chain A: S.80, I.82, L.83, R.86, R.96, R.111, Y.118, D.218 Chain B: K.163, D.194 Ligands: MN.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.80, A:S.80, A:Y.118, B:K.163 Water bridges: A:R.96 Salt bridges: A:R.86, A:R.86, A:R.96, A:R.111, A:R.111, B:K.163 ICT.4: 11 residues within 4Å: Chain A: K.163, D.194 Chain B: S.80, I.82, L.83, R.86, R.96, R.111, Y.118, D.218 Ligands: MN.5 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:K.163, B:S.80, B:S.80 Salt bridges: A:K.163, B:R.86, B:R.86, B:R.96, B:R.111, B:R.111 Water bridges: B:R.96

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: ICT.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: ICT.4 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.194, B:D.218, H2O.1, H2O.1

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

MPD.3: 7 residues within 4Å: Chain A: I.12, S.230, H.250, A.253, A.262, N.263, D.301 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.12, A:A.253, A:D.301 Hydrogen bonds: A:N.263, A:D.301 MPD.6: 7 residues within 4Å: Chain B: I.12, S.230, H.250, A.253, A.262, N.263, D.301 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.12, B:A.253, B:D.301 Hydrogen bonds: B:N.263, B:D.301

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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