7JMK

GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32

PDB DOI: https://doi.org/10.2210/pdb7JMK/pdb

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

Deposited: 2020-08-01 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: 2.50 Å
R-Value Free: 0.269
R-Value Work: 0.240
R-Value Observed: 0.241

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 149.99 kDa
Atom Count: 10,081
Modelled Residue Count: 1,327
Deposited Residue Count: 1,400
Unique protein chains: 3

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, C	305	Sus scrofa	Mutation(s): 0 Gene Names: SUCLG1 EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data)
UniProt
Find proteins for O19069 (Sus scrofa) Explore O19069 Go to UniProtKB: O19069
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O19069
Sequence Annotations Expand
Reference Sequence

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(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	Sus scrofa	Mutation(s): 0 Gene Names: SUCLG2 EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa) Explore P53590 Go to UniProtKB: P53590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53590
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial	D	395	Sus scrofa	Mutation(s): 0 Gene Names: SUCLG2 EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa) Explore P53590 Go to UniProtKB: P53590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	D	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.269
R-Value Work: 0.240
R-Value Observed: 0.241
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.762	α = 90
b = 99.762	β = 90
c = 134.206	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-10

Deposition Author(s):

Huang, J.

Fraser, M.E.

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

Revision History (Full details and data files)

Version 1.0: 2021-03-10
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary