7JMK

GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialA, C305Sus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO19069
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate--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
Entity Groups  
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UniProt GroupP53590
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrialD395Sus scrofaMutation(s): 0 
Gene Names: SUCLG2
EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa)
Explore P53590 
Go to UniProtKB:  P53590
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53590
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.762α = 90
b = 99.762β = 90
c = 134.206γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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