9IWD | pdb_00009iwd

High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative

• PDB DOI: https://doi.org/10.2210/pdb9IWD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-25 Released: 2025-08-06 
• Deposition Author(s): Cao, H., Zhang, X., Ren, Y., Wan, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.227 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative

Cao, H., Zhang, X., Ren, Y., Wan, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.25 kDa 
• Atom Count: 2,608 
• Modeled Residue Count: 323 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase 3	A	340	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TDH3, GPD3, YGR192C, G7576 EC: 1.2.1.12
UniProt
Find proteins for P00359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00359  Go to UniProtKB:  P00359

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EA6 (Subject of Investigation/LOI)	B [auth A]	ethyl 4-[(4-chlorophenyl)amino]-4-oxidanylidene-butanoate C12 H14 Cl N O3 XUFMMGCZRKBIFB-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.227 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.455	α = 90
b = 116.455	β = 90
c = 112.627	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Cao, H., Zhang, X., Ren, Y., Wan, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177036
National Natural Science Foundation of China (NSFC)	China	22377030
National Natural Science Foundation of China (NSFC)	China	22373039

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release