8ST6 | pdb_00008st6

Hsa Siglec + Unique domains bound to Neu5Gc alpha2,3 Gal beta OMe

• PDB DOI: https://doi.org/10.2210/pdb8ST6/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptococcus gordonii str. Challis substr. CH1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-05-09 Released: 2024-05-15 
• Deposition Author(s): Stubbs, H.E., Iverson, T.M.
• Funding Organization(s): Department of Veterans Affairs (VA, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Hsa Siglec + Unique domains bound to Neu5Gc alpha2,3 Gal beta OMe

Stubbs, H.E., Iverson, T.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.38 kDa 
• Atom Count: 1,909 
• Modeled Residue Count: 204 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptococcal hemagglutinin	A	234	Streptococcus gordonii str. Challis substr. CH1	Mutation(s): 0  Gene Names: hsa
UniProt
Find proteins for A8AWU7 (Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)) Explore A8AWU7  Go to UniProtKB:  A8AWU7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
USR (Subject of Investigation/LOI)	D [auth A]	methyl 3-O-[3,5-dideoxy-5-(2-hydroxyacetamido)-L-glycero-alpha-D-gulo-non-2-ulopyranonosyl]-beta-D-talopyranoside C18 H31 N O15 UWADXVSOESDFFH-VKYAEBFESA-N
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.067	α = 90
b = 57.695	β = 90
c = 75.952	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Stubbs, H.E., Iverson, T.M.

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Funding Organization	Location	Grant Number
Department of Veterans Affairs (VA, United States)	United States	R01AI130684
Department of Veterans Affairs (VA, United States)	United States	R01AI106987
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137458
American Heart Association	United States	14GRNT20390021

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release