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
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 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 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

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 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 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]