GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2.

Lira-Navarrete, E.Iglesias-Fernandez, J.Zandberg, W.F.Companon, I.Kong, Y.Corzana, F.Pinto, B.M.Clausen, H.Peregrina, J.M.Vocadlo, D.Rovira, C.Hurtado-Guerrero, R.

(2014) Angew Chem Int Ed Engl 53: 8206

  • DOI: https://doi.org/10.1002/anie.201402781
  • Primary Citation of Related Structures:  
    4D0T, 4D0Z, 4D11

  • PubMed Abstract: 

    The retaining glycosyltransferase GalNAc-T2 is a member of a large family of human polypeptide GalNAc-transferases that is responsible for the post-translational modification of many cell-surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum-mechanics/molecular-mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic-electronic level of detail. Our study provides a detailed structural rationale for an ordered bi-bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front-face SN i-type reaction in which the substrate N-acetyl sugar substituent coordinates efficient glycosyl transfer.

  • Organizational Affiliation

    Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Fundacion ARAID, Edificio Pignatelli 36 (Spain).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
571Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q10471 (Homo sapiens)
Explore Q10471 
Go to UniProtKB:  Q10471
PHAROS:  Q10471
GTEx:  ENSG00000143641 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10471
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDEG [auth X],
H [auth Y]
6Homo sapiensMutation(s): 0 
Find proteins for Q6FI18 (Homo sapiens)
Explore Q6FI18 
Go to UniProtKB:  Q6FI18
Entity Groups  
UniProt GroupQ6FI18
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HWU

Download Ideal Coordinates CCD File 
FB [auth E]
GA [auth C]
IB [auth F]
JA [auth D]
U [auth A]
FB [auth E],
GA [auth C],
IB [auth F],
JA [auth D],
U [auth A],
W [auth B]
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C17 H27 N3 O16 P2 S
Query on BBK

Download Ideal Coordinates CCD File 
EB [auth E],
FA [auth B],
KA [auth D],
T [auth A]
C8 H15 N O5 S
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth E]
BA [auth B]
BB [auth E]
CA [auth B]
AA [auth B],
AB [auth E],
BA [auth B],
BB [auth E],
CA [auth B],
CB [auth E],
DA [auth B],
DB [auth E],
EA [auth B],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth B],
ZA [auth E]
C2 H6 O2
Query on MN

Download Ideal Coordinates CCD File 
GB [auth E]
HA [auth C]
HB [auth F]
I [auth A]
IA [auth D]
GB [auth E],
HA [auth C],
HB [auth F],
I [auth A],
IA [auth D],
V [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.485α = 90
b = 121.143β = 90
c = 249.387γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2014-08-13
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary