6G4Q | pdb_00006g4q

Structure of human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2

• PDB DOI: https://doi.org/10.2210/pdb6G4Q/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-28 Released: 2018-04-11 
• Deposition Author(s): Bailey, H.J., Shrestha, L., Rembeza, E., Sorrell, F.J., Newman, J., Strain-Damerell, C., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.254 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Structure of human ADP-forming succinyl-CoA ligase complex SUCLG1-SUCLA2

Bailey, H.J., Shrestha, L., Rembeza, E., Sorrell, F.J., Strain-Damerell, C., Burgess-Brown, N., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 78.15 kDa 
• Atom Count: 5,144 
• Modeled Residue Count: 698 
• Deposited Residue Count: 722 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial	A	307	Homo sapiens	Mutation(s): 0  Gene Names: SUCLG1 EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data), 6.2.1.9 (UniProt), 6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P53597 (Homo sapiens) Explore P53597  Go to UniProtKB:  P53597
PHAROS:  P53597 GTEx:  ENSG00000163541

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial	B	415	Homo sapiens	Mutation(s): 0  Gene Names: SUCLA2 EC: 6.2.1.5 (PDB Primary Data), 6.2.1.9 (UniProt), 6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2R7 (Homo sapiens) Explore Q9P2R7  Go to UniProtKB:  Q9P2R7
PHAROS:  Q9P2R7 GTEx:  ENSG00000136143

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	A	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.254 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.2	α = 90
b = 130.2	β = 90
c = 119.772	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Bailey, H.J., Shrestha, L., Rembeza, E., Sorrell, F.J., Newman, J., Strain-Damerell, C., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary