9RAV | pdb_00009rav

Streptococcus pyogenes GapN in complex with 4-hydroxypyridazine

PDB DOI: https://doi.org/10.2210/pdb9RAV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus pyogenes
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2025-05-21 Released: 2025-11-19
Deposition Author(s): Wirsing, R., Schindelin, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.207 (Depositor), 0.215 (DCC)
R-Value Work:
0.168 (Depositor), 0.179 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Streptococcus pyogenes GapN in complex with 4-hydroxypyridazine (R76)

Wirsing, R., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 425.97 kDa
Atom Count: 33,308
Modeled Residue Count: 3,795
Deposited Residue Count: 3,968
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	496	Streptococcus pyogenes	Mutation(s): 0 Gene Names: E0F67_08075 EC: 1.2.1.9
UniProt
Find proteins for A0A4U9C786 (Streptococcus pyogenes) Explore A0A4U9C786 Go to UniProtKB: A0A4U9C786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4U9C786
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JDY (Subject of Investigation/LOI) Query on A1JDY Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth G]	CA [auth H] J [auth A] L [auth B] N [auth C] R [auth D] CA [auth H], J [auth A], L [auth B], N [auth C], R [auth D], V [auth E], X [auth F], Y [auth G]	4-hydroxypyridazine C₄ H₄ N₂ O VHVUTJZQFZBIRR-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth G] Interactions & Density Focus chain CA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth H] SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G]	AA [auth G] BA [auth H] EA [auth H] I [auth A] M [auth B] AA [auth G], BA [auth H], EA [auth H], I [auth A], M [auth B], O [auth C], P [auth C], Q [auth D], S [auth D], T [auth D], U [auth E], W [auth F], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain EA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain EA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain FA [auth H] SDF format, chain K [auth A] MOL2 format, chain DA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain K [auth A] mmCIF format, chain DA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain K [auth A]	DA [auth H], FA [auth H], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain FA [auth H] Focus chain K [auth A] Interactions & Density Focus chain DA [auth H] Focus chain FA [auth H] Focus chain K [auth A]