9RAU | pdb_00009rau

Streptococcus pyogenes GapN in complex with pyrimidine-5-amine

PDB DOI: https://doi.org/10.2210/pdb9RAU/pdb

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

Deposited: 2025-05-21 Released: 2025-07-30
Deposition Author(s): Wirsing, R., Schindelin, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.219 (Depositor), 0.184 (DCC)
R-Value Work:
0.175 (Depositor), 0.182 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

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 pyrimidine-5-amine

Wirsing, R., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 428.89 kDa
Atom Count: 31,879
Modeled Residue Count: 3,796
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain R [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain R [auth B]	BA [auth D], R [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth D] Focus chain R [auth B]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain FA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain V [auth C] SDF format, chain VA [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth H] mmCIF format, chain CA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth H]	CA [auth D] FA [auth E] K [auth A] KA [auth F] Q [auth B] CA [auth D], FA [auth E], K [auth A], KA [auth F], Q [auth B], QA [auth G], V [auth C], VA [auth H]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain FA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain V [auth C] Focus chain VA [auth H] Interactions & Density Focus chain CA [auth D] Focus chain FA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain V [auth C] Focus chain VA [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain EA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth G] SDF format, chain P [auth B] SDF format, chain PA [auth G] SDF format, chain T [auth C] SDF format, chain TA [auth H] SDF format, chain UA [auth H] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain UA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D]	AA [auth D] EA [auth E] I [auth A] IA [auth F] JA [auth F] AA [auth D], EA [auth E], I [auth A], IA [auth F], JA [auth F], M [auth A], O [auth B], OA [auth G], P [auth B], PA [auth G], T [auth C], TA [auth H], UA [auth H], W [auth C], X [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth A] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain T [auth C] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain W [auth C] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain M [auth A] Focus chain O [auth B] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain T [auth C] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain W [auth C] Focus chain X [auth D] Focus chain Z [auth D]
T5V (Subject of Investigation/LOI) Query on T5V Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain NA [auth G] SDF format, chain S [auth C] SDF format, chain SA [auth H] SDF format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth H] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth H] mmCIF format, chain Y [auth D]	DA [auth E] HA [auth F] J [auth A] N [auth B] NA [auth G] DA [auth E], HA [auth F], J [auth A], N [auth B], NA [auth G], S [auth C], SA [auth H], Y [auth D]	pyrimidin-5-amine C₄ H₅ N₃ FVLAYJRLBLHIPV-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain S [auth C] Focus chain SA [auth H] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth G] Focus chain S [auth C] Focus chain SA [auth H] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain MA [auth F] SDF format, chain RA [auth G] SDF format, chain U [auth C] SDF format, chain WA [auth H] SDF format, chain XA [auth H] MOL2 format, chain GA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain RA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain WA [auth H] MOL2 format, chain XA [auth H] mmCIF format, chain GA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain MA [auth F] mmCIF format, chain RA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain WA [auth H] mmCIF format, chain XA [auth H]	GA [auth E] L [auth A] LA [auth F] MA [auth F] RA [auth G] GA [auth E], L [auth A], LA [auth F], MA [auth F], RA [auth G], U [auth C], WA [auth H], XA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain RA [auth G] Focus chain U [auth C] Focus chain WA [auth H] Focus chain XA [auth H] Interactions & Density Focus chain GA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain RA [auth G] Focus chain U [auth C] Focus chain WA [auth H] Focus chain XA [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain YA [auth H] MOL2 format, chain YA [auth H] mmCIF format, chain YA [auth H]	YA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain YA [auth H] Interactions & Density Focus chain YA [auth H]