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
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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 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

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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
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]