6WCV | pdb_00006wcv

Tartryl-CoA bound to human GTP-specific succinyl-CoA synthetase

• PDB DOI: https://doi.org/10.2210/pdb6WCV/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-31 Released: 2020-07-15 
• 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: 1.52 Å
• R-Value Free: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Tartryl-CoA inhibits succinyl-CoA synthetase

Huang, J., Fraser, M.E.

(2020) Acta Crystallogr F Struct Biol Commun 76: 302

• DOI: https://doi.org/10.1107/S2053230X20008201

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: 77.05 kDa 
• Atom Count: 5,985 
• Modeled Residue Count: 699 
• 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): 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 [GDP-forming] subunit beta, mitochondrial	B	395	Homo sapiens	Mutation(s): 0  Gene Names: SUCLG2 EC: 6.2.1.4 (PDB Primary Data), 6.2.1 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TUY (Subject of Investigation/LOI)	C [auth A]	(3S,5S,9R,20R,21R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,20, 21-pentahydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphadocosan-22-oic acid 3,5-dioxide (non-preferred name) C25 H40 N7 O21 P3 S WLCAXJYUSAHDIC-HNBYOPSBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.069	α = 90
b = 82.465	β = 102.87
c = 49.276	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-15 
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: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description