4Q56

Structure of Helix aspersa agglutinin with natural glycosylation and N-acetyl-alpha-D-galactosamine (GalNAc)

• PDB DOI: https://doi.org/10.2210/pdb4Q56/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Cornu aspersum
• Mutation(s): No 


• Deposited: 2014-04-16 Released: 2015-10-14 
• Deposition Author(s): Pietrzyk, A.J., Bujacz, A., Bujacz, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.168 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 12.76 kDa 
• Atom Count: 1,037 
• Modelled Residue Count: 101 
• Deposited Residue Count: 101 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix aspersa agglutinin (HAA)	A	101	Cornu aspersum	Mutation(s): 0
UniProt
Find proteins for A0A0R4I963 (Cornu aspersum) Explore A0A0R4I963  Go to UniProtKB:  A0A0R4I963

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-[beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G52988LW GlyCosmos:  G52988LW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	D [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.168 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.9	α = 90
b = 47.9	β = 90
c = 281.53	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Pietrzyk, A.J., Bujacz, A., Bujacz, G.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 2.0: 2019-12-25
  Changes: Data collection, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary