7JH0

Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Schistosoma mansoni

• PDB DOI: https://doi.org/10.2210/pdb7JH0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Schistosoma mansoni
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-20 Released: 2021-02-17 
• Deposition Author(s): Boreiko, S., Silva, M., Iulek, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.273 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth.

Boreiko, S., Silva, M., Iulek, J.

(2021) Biochimie 184: 18-25

• PubMed: 33524435 
• DOI: https://doi.org/10.1016/j.biochi.2021.01.014
• Primary Citation of Related Structures:  
  7JH0


• PubMed Abstract: 
  

  The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase from Schistosoma mansoni (SmGAPDH) is characterized as a therapeutical target for schistosomiasis. In this context, we report here the experimental structure, structural analyses and comparisons of SmGAPDH, the first one from a Platyhelminth. The enzyme was expressed, purified and assayed for crystallization, what allowed the obtainment of crystals of sufficient quality to collect X-ray diffraction data up to 2.51 Å resolution. SmGAPDH is the only GAPDH to present the sequence NNR (its residues 114-116) which leads to (especially R116) a hydrogen bond network that possibly reflects on the flexibility of residues to interact with the adenine part of NAD ⁺ , speculated to be important for differential drug design.

---

Organizational Affiliation: 

Department of Chemistry, State University of Ponta Grossa, Ponta Grossa - PR, 84030-900, Brazil.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 146.73 kDa 
• Atom Count: 10,188 
• Modelled Residue Count: 1,352 
• Deposited Residue Count: 1,352 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C	338	Schistosoma mansoni	Mutation(s): 0  EC: 1.2.1.12
UniProt
Find proteins for P20287 (Schistosoma mansoni) Explore P20287  Go to UniProtKB:  P20287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	D	338	Schistosoma mansoni	Mutation(s): 0  EC: 1.2.1.12
UniProt
Find proteins for P20287 (Schistosoma mansoni) Explore P20287  Go to UniProtKB:  P20287

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth A], I [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	H [auth B], K [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSP	A, B, C	L-PEPTIDE LINKING	C3 H8 N O5 P S		CYS
CSD	D	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.273 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.123	α = 90
b = 80.123	β = 90
c = 417.015	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data processing
PHENIX	model building
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Boreiko, S., Silva, M., Iulek, J.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description