9RB1 | pdb_00009rb1

Streptococcus pyogenes GapN in complex with 2-cyanoacetamide

PDB DOI: https://doi.org/10.2210/pdb9RB1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptococcus pyogenes
Expression System: Escherichia coli
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: 1.61 Å
R-Value Free:
0.193 (Depositor), 0.195 (DCC)
R-Value Work:
0.157 (Depositor), 0.161 (DCC)
R-Value Observed:
0.159 (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 2-cyanoacetamide

Wirsing, R., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 427.05 kDa
Atom Count: 33,371
Modeled Residue Count: 3,796
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 Q99Z67 (Streptococcus pyogenes serotype M1) Explore Q99Z67 Go to UniProtKB: Q99Z67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99Z67
Sequence Annotations Expand
Reference Sequence

Small Molecules

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