8QHN | pdb_00008qhn

Streptococcus pyogenes GapN in complex with NADPH and erythrose-4-phosphate

PDB DOI: https://doi.org/10.2210/pdb8QHN/pdb

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

Deposited: 2023-09-08 Released: 2025-06-04
Deposition Author(s): Wirsing, R., Schindelin, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.211 (Depositor), 0.211 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (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 NADPH and erythrose-4-phosphate

Wirsing, R., Schindelin, H.

To be published.

Macromolecule Content

Total Structure Weight: 409.02 kDa
Atom Count: 31,715
Modeled Residue Count: 3,798
Deposited Residue Count: 3,805
Unique protein chains: 2

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, E, F A, B, C, E, F, G, H	475	Streptococcus pyogenes	Mutation(s): 0 Gene Names: E0F67_08075
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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	D	480	Streptococcus pyogenes	Mutation(s): 0 Gene Names: E0F67_08075
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 L [auth B] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	I [auth A], L [auth B], T [auth E], W [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain T [auth E] Focus chain W [auth F]
E4P (Subject of Investigation/LOI) Query on E4P Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ERYTHOSE-4-PHOSPHATE C₄ H₉ O₇ P NGHMDNPXVRFFGS-IUYQGCFVSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth H] SDF format, chain CA [auth H] SDF format, chain DA [auth H] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G]	AA [auth G] BA [auth H] CA [auth H] DA [auth H] K [auth A] AA [auth G], BA [auth H], CA [auth H], DA [auth H], K [auth A], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth D], U [auth E], V [auth F], X [auth F], Y [auth G], Z [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain X [auth F] Focus chain Y [auth G] Focus chain Z [auth G]