9RAZ | pdb_00009raz

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


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.

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, D, E
A, B, C, D, E, F, G, H
496Streptococcus pyogenesMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4U9C786
Sequence Annotations
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  • 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],
J [auth B],
L [auth E],
P [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
G3H (Subject of Investigation/LOI)
Query on G3H

Download Ideal Coordinates CCD File 
M [auth F]GLYCERALDEHYDE-3-PHOSPHATE
C3 H7 O6 P
LXJXRIRHZLFYRP-VKHMYHEASA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth D],
N [auth F],
O [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.15α = 77.06
b = 97.435β = 78.19
c = 100.71γ = 68.92
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release