5C7O

Structure of human testis-specific glyceraldehyde-3-phosphate dehydrogenase holo form with NAD+

• PDB DOI: https://doi.org/10.2210/pdb5C7O/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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.166 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

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.

---

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: 74.85 kDa 
• Atom Count: 5,945 
• Modelled Residue Count: 670 
• Deposited Residue Count: 670 
• 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 P]	335	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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth O], E [auth P]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	D [auth O], F [auth P]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.166 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.442	α = 90
b = 71.741	β = 123.01
c = 80.844	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection