5C7L

Structure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase apo form

• PDB DOI: https://doi.org/10.2210/pdb5C7L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-24 Released: 2016-03-09 
• Deposition Author(s): Betts, L., Machius, M., Danshina, P., O'Brien, D.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structural analyses to identify selective inhibitors of glyceraldehyde 3-phosphate dehydrogenase-S, a sperm-specific glycolytic enzyme.

Danshina, P.V., Qu, W., Temple, B.R., Rojas, R.J., Miley, M.J., Machius, M., Betts, L., O'Brien, D.A.

(2016) Mol Hum Reprod 22: 410-426

• PubMed: 26921398 
• DOI: https://doi.org/10.1093/molehr/gaw016
• Primary Citation of Related Structures:  
  5C7I, 5C7L, 5C7O


• PubMed Abstract: 
  

  Detailed structural comparisons of sperm-specific glyceraldehyde 3-phosphate dehydrogenase, spermatogenic (GAPDHS) and the somatic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) isozyme should facilitate the identification of selective GAPDHS inhibitors for contraceptive development.

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Organizational Affiliation: 

Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.

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: 73.48 kDa 
• Atom Count: 5,594 
• Modelled Residue Count: 672 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, testis-specific	A [auth O], B [auth R]	336	Homo sapiens	Mutation(s): 0  Gene Names: GAPDHS, GAPD2, GAPDH2, GAPDS, HSD-35, HSD35 EC: 1.2.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for O14556 (Homo sapiens) Explore O14556  Go to UniProtKB:  O14556
PHAROS:  O14556 GTEx:  ENSG00000105679

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A [auth O], B [auth R]	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.888	α = 90
b = 86.888	β = 90
c = 159.606	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Betts, L., Machius, M., Danshina, P., O'Brien, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	--

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence