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Crsytal structure of pp-GalNAc-T10 with UDP, GalNAc and Mn2+
 
 
DOI:10.2210/pdb2d7i/pdb
2D7I
 
Primary Citation
spinning wheel
 
 
  •  
    Move Section Molecular Description Hide
    Classification: Transferase
    Structure Weight: 67020.03
     
    Molecule:Polypeptide N-acetylgalactosaminyltransferase 10
    Polymer:1Type:polypeptide(L)Length:570
    Chains:A
    EC#:2.4.1.41 Go to IUBMB EC entry  
    Fragment:residues 40-603
     
     
  •  
    Move Section Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens Go to NCBI Taxonomy entry Common Name: Human Expression System: Pichia pastoris  
    Polymer: 2
    Scientific Name: Synthetic construct Go to NCBI Taxonomy entry  
     
     
  •  
    Move Section Related PDB Entries Hide
    Id Details
    2D7R  the same protein complexed with GalNAc-Ser 
     
     
  •  
    Move Section Ligand Chemical Component Hide
    Identifier Name Formula Interaction View Links
    MN     MANGANESE (II) ION Mn 3DLigand Explorer Link out to Ligand Expos:MN Link out to SuperLigands:MN Link out to SuperHapten:MN
    NAG     N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 3DLigand Explorer Link out to Ligand Expos:NAG Link out to SuperLigands:NAG Link out to SuperHapten:NAG
    NGA     N-ACETYL-D-GALACTOSAMINE C8 H15 N O6 3DLigand Explorer Link out to Ligand Expos:NGA Link out to SuperLigands:NGA Link out to SuperHapten:NGA
    UDP     URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 3DLigand Explorer Link out to Ligand Expos:UDP Link out to SuperLigands:UDP Link out to SuperHapten:UDP
     
     
  •  
    Move Section Modified Residues Hide
    Identifier Name Formula Interaction View Links
    UDP URIDINE-5'-DIPHOSPHATE(type: rnaLinking) C9 H14 N2 O12 P2 3D Ligand Explorer Link out to Ligand Expos:UDP Link out to SuperLigands:UDP Link out to SuperHapten:UDP 2D
     
     
  •  
    Move Section Derived Data Hide
     
     
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  •  
    Move Section Deposition Summary Hide
    Authors:   Kubota, T.,   Shiba, T.,   Sugioka, S.,   Kato, R.,   Wakatsuki, S.,   Narimatsu, H.

    Deposition:   2005-11-21
    Release:   2006-11-07
    Last Modified (REVDAT):   2009-02-24
     
     
  •  
    Move Section Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Experimental Data:   Download Structure Factors  [ EDS External Link to EDS ]
    View a histogram of Resolution Resolution[Å]: 2.50
    R-Value: 0.220 (obs.)
    R-Free: 0.267
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 79.86 α = 90.00 
    b = 133.38 β = 90.00 
    c = 138.71 γ = 90.00