SMTL ID : 6hsp.2 (1 other biounit)

Crystal structure of the zebrafish peroxisomal SCP2-thiolase (type-1) in complex with CoA and octanoyl-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: K.25, R.46, P.197, Y.198 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.25, A:R.46, A:R.46 Water bridges: A:E.42, A:E.42 GOL.4: 4 residues within 4Å: Chain B: K.25, R.46, P.197, Y.198 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.25, B:R.46, B:R.46 Water bridges: B:E.42, B:E.42

2 x CO8: OCTANOYL-COENZYME A(Non-covalent)

CO8.2: 16 residues within 4Å: Chain A: K.28, Y.67, C.95, M.125, A.160, F.201, R.214, L.222, L.223, C.225, C.226, P.227, F.309, H.356, L.358 Ligands: COA.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.214, A:C.225, A:C.226 Salt bridges: A:K.28, A:R.214 CO8.5: 16 residues within 4Å: Chain B: K.28, Y.67, C.95, M.125, A.160, F.201, R.214, L.222, L.223, C.225, C.226, P.227, F.309, H.356, L.358 Ligands: COA.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.67, B:R.214, B:C.225, B:C.226 Salt bridges: B:K.28, B:R.214

2 x COA: COENZYME A(Non-covalent)

COA.3: 14 residues within 4Å: Chain A: K.28, C.95, A.160, F.164, F.201, R.214, L.222, L.223, C.225, C.226, P.227, T.228, F.309 Ligands: CO8.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.214, A:C.225, A:C.226, A:T.228 Salt bridges: A:K.28, A:R.214 COA.6: 14 residues within 4Å: Chain B: K.28, C.95, A.160, F.164, F.201, R.214, L.222, L.223, C.225, C.226, P.227, T.228, F.309 Ligands: CO8.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.214, B:C.225, B:C.226, B:T.228 Salt bridges: B:K.28, B:R.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiema, T.R. et al., The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry. Biochem. J. (2019)

Release Date

2019-01-02

Peptides

SCP2-thiolase (type-1): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

SCP2-thiolase (type-1)

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