5C7I

Mouse sperm Glyceraldehyde-3-phosphate dehydrogenase: apo enzyme

PDB DOI: https://doi.org/10.2210/pdb5C7I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-24 Released: 2016-03-09
Deposition Author(s): Danshina, P., Betts, L., O'Brien, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.207
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 72.42 kDa
Atom Count: 5,537
Modelled Residue Count: 666
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, testis-specific	A [auth O], B [auth R]	333	Mus musculus	Mutation(s): 0 Gene Names: Gapdhs, Gapd-s, Gapds EC: 1.2.1.12
UniProt
Find proteins for Q64467 (Mus musculus) Explore Q64467 Go to UniProtKB: Q64467
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q64467
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A [auth O], B [auth R]	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.207
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.717	α = 90
b = 86.717	β = 90
c = 158.358	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-09
Type: Initial release
Version 1.1: 2016-06-15
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.