Download MendeleySecond distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase
Huang, J., Fraser, M.E.(2021) Acta Crystallogr D Biol Crystallogr 77: 357-368
7JFP
GTP-specific succinyl-CoA synthetase complexed with Mg-GDP, phosphohistidine loop pointing towards nucleotide binding site
- PDB DOI: https://doi.org/10.2210/pdb7JFP/pdb
- Classification: LIGASE
- Organism(s): Sus scrofa
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-07-17 Released: 2021-03-10
- Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.293
- R-Value Work: 0.240
- R-Value Observed: 0.242
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial | 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 AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial | 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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP (Subject of Investigation/LOI) Query on GDP | D [auth B] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N |  | ||
| GOL Query on GOL | C [auth A], E [auth B], F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MG Query on MG | G [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CME Query on CME | B | L-PEPTIDE LINKING | C5 H11 N O3 S2 |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.293
- R-Value Work: 0.240
- R-Value Observed: 0.242
- Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.645 | α = 90 |
| b = 99.645 | β = 90 |
| c = 134.262 | γ = 120 |
| Software Name | Purpose |
|---|---|
| xia2 | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| xia2 | data reduction |
| PHASER | phasing |
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: 2024-11-20
Changes: Structure summary
