SMTL ID : 1dxy.1 (1 other biounit)

STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.3, COI.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.76, A:V.77, A:G.78 Salt bridges: A:R.234 SO4.2: 6 residues within 4Å: Chain A: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.99 Water bridges: A:S.325, A:S.325 Salt bridges: A:H.314 SO4.5: 7 residues within 4Å: Chain B: N.76, V.77, G.78, Y.100, R.234 Ligands: NAD.7, COI.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.76, B:V.77, B:G.78, B:Y.100 Salt bridges: B:R.234 SO4.6: 6 residues within 4Å: Chain B: V.97, P.98, A.99, F.310, H.314, T.326 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.99 Water bridges: B:S.325, B:S.325 Salt bridges: B:H.314

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

NAD.3: 27 residues within 4Å: Chain A: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.1, COI.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.105 Hydrogen bonds: A:H.155, A:I.156, A:G.157, A:Y.177, A:V.205, A:G.207, A:N.211, A:N.211, A:R.234, A:D.258, A:D.258, A:A.297, A:Y.298 Water bridges: A:G.154, A:H.155, A:H.155, A:H.155 Salt bridges: A:H.155, A:H.155 NAD.7: 27 residues within 4Å: Chain B: Y.100, I.105, G.152, G.154, H.155, I.156, G.157, Y.174, D.175, P.176, Y.177, H.204, V.205, P.206, G.207, N.211, I.214, T.232, A.233, R.234, D.258, T.259, H.295, A.297, Y.298 Ligands: SO4.5, COI.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.105 Hydrogen bonds: B:H.155, B:I.156, B:G.157, B:Y.177, B:V.205, B:G.207, B:N.211, B:N.211, B:R.234, B:D.258, B:A.297, B:Y.298 Water bridges: B:T.153, B:G.154, B:H.155, B:H.155 Salt bridges: B:H.155, B:H.155

2 x COI: 2-OXO-4-METHYLPENTANOIC ACID(Non-covalent)

COI.4: 10 residues within 4Å: Chain A: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.1, NAD.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.298 Hydrogen bonds: A:N.76, A:V.77, A:G.78, A:R.234, A:R.234 Salt bridges: A:R.234 COI.8: 10 residues within 4Å: Chain B: R.9, N.76, V.77, Y.100, R.234, H.295, Y.298, M.307 Ligands: SO4.5, NAD.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.298 Hydrogen bonds: B:N.76, B:V.77, B:G.78, B:Y.100, B:R.234, B:R.234 Salt bridges: B:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dengler, U. et al., Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. J.Mol.Biol. (1997)

Release Date

1997-06-16

Peptides

D-2-HYDROXYISOCAPROATE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

D-2-HYDROXYISOCAPROATE DEHYDROGENASE

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