6GX1 | pdb_00006gx1

Blood group synthase AAGlyB in complex with UDP-GalNAc and cryoprotected with PEG 3350

• PDB DOI: https://doi.org/10.2210/pdb6GX1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-06-26 Released: 2019-07-10 
• Deposition Author(s): Rocha, J., Royant, A.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Blood group synthase AAGlyB in complex with UDP-GalNAc and cryoprotected with PEG 3350

Rocha, J., Batot, G.O., Palcic, M.M., Breton, C., Royant, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 36.11 kDa 
• Atom Count: 2,954 
• Modeled Residue Count: 285 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)	A	298	Homo sapiens	Mutation(s): 1  Gene Names: ABO EC: 2.4.1.40 (UniProt), 2.4.1.37 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens) Explore P16442  Go to UniProtKB:  P16442
PHAROS:  P16442

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD2	C [auth A]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
UDP	D [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.198 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.635	α = 90
b = 148.386	β = 90
c = 79.816	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Rocha, J., Royant, A.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-13-BSV8-0011-02

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description