9RAZ | pdb_00009raz

Streptococcus pyogenes GapN in complex with NADP and glyceraldehyde-3-phosphate

PDB DOI: https://doi.org/10.2210/pdb9RAZ/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: 1.38 Å
R-Value Free:
0.179 (Depositor), 0.180 (DCC)
R-Value Work:
0.154 (Depositor), 0.156 (DCC)
R-Value Observed:
0.155 (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 NADP and glyceraldehyde-3-phosphate

Wirsing, R., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 427.09 kDa
Atom Count: 33,909
Modeled Residue Count: 3,800
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 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
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth E] SDF format, chain P [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth E] MOL2 format, chain P [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth E] mmCIF format, chain P [auth F]	I [auth A], J [auth B], L [auth E], P [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth E] Focus chain P [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth E] Focus chain P [auth F]
G3H (Subject of Investigation/LOI) Query on G3H Download Ideal Coordinates CCD File SDF format, chain M [auth F] MOL2 format, chain M [auth F] mmCIF format, chain M [auth F]	M [auth F]	GLYCERALDEHYDE-3-PHOSPHATE C₃ H₇ O₆ P LXJXRIRHZLFYRP-VKHMYHEASA-N		Interactions Focus chain M [auth F] Interactions & Density Focus chain M [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain N [auth F] SDF format, chain O [auth F] MOL2 format, chain K [auth D] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] mmCIF format, chain K [auth D] mmCIF format, chain N [auth F] mmCIF format, chain O [auth F]	K [auth D], N [auth F], O [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain K [auth D] Focus chain N [auth F] Focus chain O [auth F]