8QHN | pdb_00008qhn

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


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
A, B, C, E, F
A, B, C, E, F, G, H
475Streptococcus pyogenesMutation(s): 0 
Gene Names: E0F67_08075
UniProt
Find proteins for A0A4U9C786 (Streptococcus pyogenes)
Explore A0A4U9C786 
Go to UniProtKB:  A0A4U9C786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4U9C786
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase480Streptococcus pyogenesMutation(s): 0 
Gene Names: E0F67_08075
UniProt
Find proteins for A0A4U9C786 (Streptococcus pyogenes)
Explore A0A4U9C786 
Go to UniProtKB:  A0A4U9C786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4U9C786
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
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
E4P (Subject of Investigation/LOI)
Query on E4P

Download Ideal Coordinates CCD File 
J [auth A]ERYTHOSE-4-PHOSPHATE
C4 H9 O7 P
NGHMDNPXVRFFGS-IUYQGCFVSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.521α = 77.766
b = 98.476β = 76.083
c = 102.981γ = 67.792
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release