9DLC | pdb_00009dlc

Streptococcus pneumoniae GAPN with G3P

• PDB DOI: https://doi.org/10.2210/pdb9DLC/pdb
• EM Map EMD-46869: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-10 Released: 2025-09-24 
• Deposition Author(s): Eunjeong, L., Elan, Z.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.56 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Biochemical, structural, and biologial studies of Streptococcus pneumoniae GapN reveal a key metabolic player necessary for host infection.

Eunjeong, L., Elan, Z.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 205.2 kDa 
• Atom Count: 14,415 
• Modeled Residue Count: 1,894 
• Deposited Residue Count: 1,896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	474	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: gapN, spr1028 EC: 1.2.1.9
UniProt
Find proteins for Q8DPS7 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DPS7  Go to UniProtKB:  Q8DPS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3H (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCERALDEHYDE-3-PHOSPHATE C3 H7 O6 P LXJXRIRHZLFYRP-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.56 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Eunjeong, L., Elan, Z.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release