7JMK | pdb_00007jmk

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 (Depositor), 0.273 (DCC)
R-Value Work:
0.240 (Depositor), 0.242 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
View more details

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
Modeled Residue Count: 1,327
Deposited Residue Count: 1,400
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 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), 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

Find similar proteins by:

| 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

Find similar proteins by:

| 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 (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 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 (Depositor), 0.273 (DCC)
R-Value Work: 0.240 (Depositor), 0.242 (DCC)
R-Value Observed: 0.241 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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