SMTL ID : 5jbx.1

Crystal structure of LiuC in complex with coenzyme A and malonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-trimer

Ligands

2 x COA: COENZYME A(Non-covalent)

COA.1: 22 residues within 4Å: Chain A: S.24, R.25, R.26, A.28, K.61, A.62, A.65, G.66, A.67, D.68, L.69, K.70, A.108, L.110, G.111, G.112, T.134, E.135, L.138, R.168 Chain C: F.250, K.253 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:A.65, C:F.250 Hydrogen bonds: A:A.65, A:A.65, A:L.69, A:R.168 Water bridges: A:A.67, C:K.253 Salt bridges: A:R.26, A:R.26, C:K.253 pi-Stacking: C:F.250, C:F.250 COA.3: 22 residues within 4Å: Chain A: F.250, K.253 Chain B: S.24, R.25, R.26, A.28, K.61, A.62, A.65, G.66, A.67, D.68, L.69, K.70, A.108, L.110, G.111, G.112, T.134, E.135, L.138, R.168 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:R.26, B:A.65, B:L.69, B:A.108 Hydrogen bonds: B:A.65, B:A.65, B:L.69, B:K.70, B:R.168, B:R.168, A:K.253 Water bridges: B:R.26, B:R.26, B:R.26, B:K.61 Salt bridges: B:R.26, B:R.26, B:K.70, A:K.253 pi-Stacking: A:F.250, A:F.250

4 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 13 residues within 4Å: Chain A: A.67, R.72, F.83, L.84, G.112, E.115, E.135, I.140, I.141, P.142, G.143, G.144 Chain C: Y.234 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.84, C:Y.234 Hydrogen bonds: A:G.112, A:G.143, A:G.144, C:Y.234, C:Y.234 Water bridges: A:A.67, A:A.67, A:R.72 Salt bridges: A:R.72 MLI.4: 14 residues within 4Å: Chain A: Y.234 Chain B: A.67, R.72, F.83, L.84, L.87, G.112, E.115, E.135, I.140, I.141, P.142, G.143, G.144 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.84, B:I.140, A:Y.234 Hydrogen bonds: B:E.135, B:G.143, B:G.144, A:Y.234 Water bridges: B:A.67, B:A.67, B:R.72, B:R.72, B:G.112 Salt bridges: B:R.72 MLI.5: 5 residues within 4Å: Chain B: R.31, K.35, M.75, E.79, A.82 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.79 Water bridges: B:K.35, B:K.35 Salt bridges: B:R.31, B:R.31, B:K.35 MLI.6: 1 residues within 4Å: Chain B: G.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bock, T. et al., The Structure of LiuC, a 3-Hydroxy-3-Methylglutaconyl CoA Dehydratase Involved in Isovaleryl-CoA Biosynthesis in Myxococcus xanthus, Reveals Insights into Specificity and Catalysis. Chembiochem (2016)

Release Date

2016-06-22

Peptides

3-hydroxybutyryl-CoA dehydratase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

3-hydroxybutyryl-CoA dehydratase