1XHB

The Crystal Structure of UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase-T1

Structural Biology Knowledgebase: 1XHB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.218

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XHB

Classification: TRANSFERASE

Total Structure Weight: 54959.08

Macromolecule Entities
Molecule Chains Length Organism Details
Polypeptide N-acetylgalactosaminyltransferase 1 A 472 Mus musculus EC#: 2.4.1.41 IUBMB
Fragment: Residues 88-559: includes catalytic subdomain A (residues 115-225), catalytic subdomain B (residues 285-347), Ricin B-type lectin (residues 429-551)
Gene Name(s): Galnt1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.218
  • Space Group: P 43
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.61 α = 90.00
b = 65.61 β = 90.00
c = 125.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-09-17
  • Released Date: 2004-10-26
  • Deposition author(s): Fritz, T.A., Hurley, J.H., Trinh, L.B., Shiloach, J., Tabak, L.A.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4