9RAS | pdb_00009ras

Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione

PDB DOI: https://doi.org/10.2210/pdb9RAS/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: 1.57 Å
R-Value Free:
0.191 (Depositor), 0.191 (DCC)
R-Value Work:
0.155 (Depositor), 0.155 (DCC)
R-Value Observed:
0.157 (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 imidazoline-2,4-dione

Wirsing, R., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 427.76 kDa
Atom Count: 34,456
Modeled Residue Count: 3,799
Deposited Residue Count: 3,968
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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
A1JDZ (Subject of Investigation/LOI) Query on A1JDZ Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth B] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth G] SDF format, chain SA [auth H] SDF format, chain T [auth C] SDF format, chain TA [auth H] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain XA [auth H] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	CA [auth D] DA [auth E] EA [auth E] HA [auth F] I [auth A] CA [auth D], DA [auth E], EA [auth E], HA [auth F], I [auth A], IA [auth F], J [auth A], MA [auth G], N [auth B], NA [auth G], O [auth B], P [auth B], PA [auth G], SA [auth H], T [auth C], TA [auth H], U [auth C], V [auth C], XA [auth H], Y [auth D], Z [auth D]	1~{H}-imidazole-2,4-diol C₃ H₄ N₂ O₂ SHFCYMWGNNAKEL-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain MA [auth G] Focus chain N [auth B] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth G] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain XA [auth H] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain MA [auth G] Focus chain N [auth B] Focus chain NA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth G] Focus chain SA [auth H] Focus chain T [auth C] Focus chain TA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain XA [auth H] Focus chain Y [auth D] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain FA [auth E] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain OA [auth G] SDF format, chain Q [auth B] SDF format, chain UA [auth H] SDF format, chain VA [auth H] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth C]	AA [auth D] BA [auth D] FA [auth E] JA [auth F] K [auth A] AA [auth D], BA [auth D], FA [auth E], JA [auth F], K [auth A], KA [auth F], L [auth A], OA [auth G], Q [auth B], UA [auth H], VA [auth H], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain FA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain UA [auth H] Focus chain VA [auth H] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain FA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain UA [auth H] Focus chain VA [auth H] Focus chain W [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain QA [auth G] SDF format, chain R [auth B] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain WA [auth H] SDF format, chain X [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth C] mmCIF format, chain GA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth C]	GA [auth E] LA [auth F] M [auth A] QA [auth G] R [auth B] GA [auth E], LA [auth F], M [auth A], QA [auth G], R [auth B], RA [auth G], S [auth B], WA [auth H], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain WA [auth H] Focus chain X [auth C] Interactions & Density Focus chain GA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain WA [auth H] Focus chain X [auth C]