7MSR | pdb_00007msr

Human E105Qa GTP-specific succinyl-CoA synthetase complexed with succinyl-phosphate, magnesium ion and desulfo-coenzyme A

PDB DOI: https://doi.org/10.2210/pdb7MSR/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 77.54 kDa
Atom Count: 5,739
Modeled Residue Count: 700
Deposited Residue Count: 710
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53597
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96I99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCA Query on DCA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DESULFO-COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ ILWZMFJBPIYQKW-IBOSZNHHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZNS (Subject of Investigation/LOI) Query on ZNS Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	4-oxo-4-(phosphonooxy)butanoic acid C₄ H₇ O₇ P NCRLTRUGOQIEKI-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B]	E [auth A], F [auth A], H [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]