4XX0

CoA bound to pig GTP-specific succinyl-CoA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of GTP-specific succinyl-CoA synthetase in complex with CoA.

Huang, J.Malhi, M.Deneke, J.Fraser, M.E.

(2015) Acta Crystallogr.,Sect.F 71: 1067-1071

  • DOI: 10.1107/S2053230X15011188

  • PubMed Abstract: 
  • Pig GTP-specific succinyl-CoA synthetase is an αβ-heterodimer. The crystal structure of the complex with the substrate CoA was determined at 2.1 Å resolution. The structure shows CoA bound to the amino-terminal domain of the α-subunit, with the free ...

    Pig GTP-specific succinyl-CoA synthetase is an αβ-heterodimer. The crystal structure of the complex with the substrate CoA was determined at 2.1 Å resolution. The structure shows CoA bound to the amino-terminal domain of the α-subunit, with the free thiol extending from the adenine portion into the site where the catalytic histidine residue resides.


    Organizational Affiliation

    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
A
313Sus scrofaMutation(s): 0 
Gene Names: SUCLG1
EC: 6.2.1.4, 6.2.1.5
Find proteins for O19069 (Sus scrofa)
Go to Gene View: SUCLG1
Go to UniProtKB:  O19069
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial
B
395Sus scrofaMutation(s): 0 
Gene Names: SUCLG2
EC: 6.2.1.4
Find proteins for P53590 (Sus scrofa)
Go to Gene View: SUCLG2
Go to UniProtKB:  P53590
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, 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 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.340α = 90.00
b = 82.500β = 104.25
c = 49.380γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada--

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-11-22
    Type: Refinement description