2D7I Transferase date Nov 21, 2005
title Crystal Structure Of Pp-Galnac-T10 With Udp, Galnac And Mn2+
authors T.Kubota, T.Shiba, S.Sugioka, R.Kato, S.Wakatsuki, H.Narimatsu
compound source
Molecule: Polypeptide N-Acetylgalactosaminyltransferase 10
Chain: A
Fragment: Residues 40-603
Synonym: Protein-Udp Acetylgalactosaminyltransferase 10, Ud
Galnac: Polypeptide N-Acetylgalactosaminyltransferase 10, Po Galnac Transferase 10, Galnac-T10, Pp-Gantase 10;
Ec: 2.4.1.41
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Smd1168
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9
symmetry Space Group: C 2 2 21
R_factor 0.215 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
79.855 133.375 138.713 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand MN, NAG, NGA, UDP enzyme Transferase E.C.2.4.1.41 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10)., Kubota T, Shiba T, Sugioka S, Furukawa S, Sawaki H, Kato R, Wakatsuki S, Narimatsu H, J Mol Biol. 2006 Jun 9;359(3):708-27. Epub 2006 Apr 19. PMID:16650853
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (2d7i.pdb1.gz) 94 Kb
  • LPC: Ligand-Protein Contacts for 2D7I
  • CSU: Contacts of Structural Units for 2D7I
  • Likely Quarternary Molecular Structure file(s) for 2D7I
  • Structure Factors (214 Kb)
  • Retrieve 2D7I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D7I from S2C, [Save to disk]
  • Re-refined 2d7i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D7I in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2D7I
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2D7I, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d7i] [2d7i_A]
  • SWISS-PROT database: [Q86SR1]
  • Domain organization of [GLT10_HUMAN] by SWISSPFAM
  • Domain found in 2D7I: [RICIN ] by SMART
  • Other resources with information on 2D7I
  • Community annotation for 2D7I at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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