6HSJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The peroxisomal zebrafish SCP2-thiolase (type-1) is a weak transient dimer as revealed by crystal structures and native mass spectrometry.

Kiema, T.R.Thapa, C.J.Laitaoja, M.Schmitz, W.Maksimainen, M.M.Fukao, T.Rouvinen, J.Janis, J.Wierenga, R.K.

(2019) Biochem. J. 476: 307-332


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SCP2-thiolase (type-1)
A
414Danio rerioMutation(s): 0 
Gene Names: scp2a (scp2)
Find proteins for Q6P4V5 (Danio rerio)
Go to UniProtKB:  Q6P4V5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SCP2-thiolase (type-1)
B
414Danio rerioMutation(s): 0 
Gene Names: scp2a (scp2)
Find proteins for Q6P4V5 (Danio rerio)
Go to UniProtKB:  Q6P4V5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.960α = 90.00
b = 80.880β = 126.29
c = 96.470γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references