7JFP

GTP-specific succinyl-CoA synthetase complexed with Mg-GDP, phosphohistidine loop pointing towards nucleotide binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase

Huang, J.Fraser, M.E.

(2021) Acta Crystallogr D Biol Crystallogr 77: 357-368


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialA305Sus scrofaMutation(s): 0 
Gene Names: SUCLG1
EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data)
UniProt
Find proteins for O19069 (Sus scrofa)
Explore O19069 
Go to UniProtKB:  O19069
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrialB395Sus scrofaMutation(s): 0 
Gene Names: SUCLG2
EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa)
Explore P53590 
Go to UniProtKB:  P53590
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], E [auth B], F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
BL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.645α = 90
b = 99.645β = 90
c = 134.262γ = 120
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada04815-2019

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release