7JH0 | pdb_00007jh0

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 (Depositor), 0.285 (DCC)
R-Value Work:
0.213 (Depositor), 0.225 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.biochi.2021.01.014
Primary Citation 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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20287
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20287
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain H [auth B]	H [auth B], K [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSP Query on CSP	A, B, C	L-PEPTIDE LINKING	C₃ H₈ N O₅ P S		CYS
CSD Query on 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 (Depositor), 0.285 (DCC)
R-Value Work: 0.213 (Depositor), 0.225 (DCC)
R-Value Observed: 0.216 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Boreiko, S.

Silva, M.

Iulek, J.

Revision History (Full details and data files)

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
Version 1.3: 2024-11-20
Changes: Structure summary