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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DPS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G3H (Subject of Investigation/LOI) Query on G3H Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCERALDEHYDE-3-PHOSPHATE C₃ H₇ O₆ P LXJXRIRHZLFYRP-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.