1ZI4

Crystal Structure of Human N-acetylgalactosaminyltransferase (GTA) Complexed with H type II Trisaccharide

• PDB DOI: https://doi.org/10.2210/pdb1ZI4/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-04-26 Released: 2005-12-13 
• Deposition Author(s): Letts, J.A., Rose, N.L., Fang, Y.R., Barry, C.H., Borisova, S.N., Seto, N.O., Palcic, M.M., Evans, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 35.69 kDa 
• Atom Count: 2,355 
• Modelled Residue Count: 264 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histo-blood group ABO system transferase (NAGAT) Includes: Glycoprotein-fucosylgalactoside alpha-N- acetylgalactosaminyltransferase	A	294	Homo sapiens	Mutation(s): 0  Gene Names: ABO EC: 2.4.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens) Explore P16442  Go to UniProtKB:  P16442
PHAROS:  P16442

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G61459JW GlyCosmos:  G61459JW GlyGen:  G61459JW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	C [auth A], E [auth A], F [auth A], G [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900036	B	H type 2 antigen, beta anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.4	α = 90
b = 150.1	β = 90
c = 79.2	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CrystalClear	data reduction
CNS	refinement
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-13 
Deposition Author(s): Letts, J.A., Rose, N.L., Fang, Y.R., Barry, C.H., Borisova, S.N., Seto, N.O., Palcic, M.M., Evans, S.V.

Revision History  

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary