7MST

Phosphorylated human E105Qa GTP-specific succinyl-CoA synthetase complexed with coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb7MST/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-05-12 Released: 2022-10-12 
• Deposition Author(s): Huang, J., Fraser, M.E.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.194 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase

Huang, J., Fraser, M.E.

(2022) Acta Crystallogr F Struct Biol Commun 78: 363-370

• DOI: https://doi.org/10.1107/S2053230X22008810

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: gel filtration

Macromolecule Content

• Total Structure Weight: 77.43 kDa 
• Atom Count: 5,839 
• Modelled Residue Count: 701 
• Deposited Residue Count: 710 
• 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	315	Homo sapiens	Mutation(s): 1  Gene Names: SUCLG1 EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data)
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 [GDP-forming] subunit beta, mitochondrial	B	395	Homo sapiens	Mutation(s): 0  Gene Names: SUCLG2 EC: 6.2.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96I99 (Homo sapiens) Explore Q96I99  Go to UniProtKB:  Q96I99
PHAROS:  Q96I99 GTEx:  ENSG00000172340

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	C [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
GOL	D [auth A], E [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	A	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS
CSS	B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.194 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.82	α = 90
b = 82.927	β = 103.47
c = 48.828	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Huang, J., Fraser, M.E.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	04815-2019

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection