6XRU | pdb_00006xru

GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions and succinates

PDB DOI: https://doi.org/10.2210/pdb6XRU/pdb

Classification: LIGASE
Organism(s): Sus scrofa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-13 Released: 2021-03-10
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: 1.40 Å
R-Value Free:
0.184 (Depositor), 0.186 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.170 (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

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

DOI: https://doi.org/10.1107/S2059798321000334

Macromolecule Content

Total Structure Weight: 77.37 kDa
Atom Count: 6,202
Modeled Residue Count: 702
Deposited Residue Count: 708
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial	A	313	Sus scrofa	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
Find proteins for O19069 (Sus scrofa) Explore O19069 Go to UniProtKB: O19069
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O19069
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial	B	395	Sus scrofa	Mutation(s): 0 Gene Names: SUCLG2 EC: 6.2.1.4 (PDB Primary Data), 6.2.1 (UniProt)
UniProt
Find proteins for P53590 (Sus scrofa) Explore P53590 Go to UniProtKB: P53590
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCA (Subject of Investigation/LOI) 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]
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]