4C2S | pdb_00004c2s

Crystal structure of the fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA P156L mutant) in complex with UDP and deoxy-H-antigen acceptor

• PDB DOI: https://doi.org/10.2210/pdb4C2S/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-08-19 Released: 2013-09-11 
• Deposition Author(s): Weadge, J.T., Palcic, M., Henriksen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.182 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Structural and Biochemical Characterization of the Human Blood Group a and B Galactosyltransferases Posessing the Pro156Leu Mutation

Weadge, J.T., Palcic, M., Henriksen, 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: 69.83 kDa 
• Atom Count: 4,959 
• Modeled Residue Count: 581 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE	A, B	292	Homo sapiens	Mutation(s): 1  EC: 2.4.1.40 (PDB Primary Data), 2.4.1.37 (PDB Primary Data)
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	D Interactions
alpha-L-fucopyranose-(1-2)-hexyl 3-deoxy-beta-D-galactopyranoside	C, D	2	N/A	N/A
Glycosylation Resources
GlyTouCan: G50243CR GlyCosmos: G50243CR

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	F [auth A], H [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MN	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.182 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.51	α = 90
b = 52.61	β = 89.97
c = 80.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Weadge, J.T., Palcic, M., Henriksen, A.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary