4D0Z Transferase Peptide date Apr 30, 2014
title Galnac-T2 Crystal Soaked With Udp-5sgalnac, Mea2 And Mangane Resolution Dataset)
authors E.Lira-Navarrete, J.Iglesias-Fernandez, W.F.Zandberg, I.Compano F.Corzana, B.M.Pinto, H.Clausen, J.M.Peregrina, D.Vocadlo, C.Rov R.Hurtado-Guerrero
compound source
Molecule: Polypeptide N-Acetylgalactosaminyltransferase 2
Chain: A, B, C, D, E, F
Synonym: Polypeptide Galnac Transferase 2, Galnac-T2, Pp-Ga
Protein-Udp Acetylgalactosaminyltransferase 2, Udp-Galnac\: Polypeptide N-Acetylgalactosaminyltransferase 2, Polypeptid Transferase T2;
Ec: 2.4.1.41
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Smd-1168
Expression_system_vector: Ppiczalphaa

Molecule: Peptide
Chain: X, Y
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Smd-1168
Expression_system_vector: Ppiczalphaa
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.485 121.143 249.387 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BBK, EDO, HWU, MN enzyme Transferase E.C.2.4.1.41 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceSubstrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N-Acetylgalactosaminyltransferase 2., Lira-Navarrete E, Iglesias-Fernandez J, Zandberg WF, Companon I, Kong Y, Corzana F, Pinto BM, Clausen H, Peregrina JM, Vocadlo DJ, Rovira C, Hurtado-Guerrero R, Angew Chem Int Ed Engl. 2014 Jun 20. doi: 10.1002/anie.201402781. PMID:24954443
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (993 Kb) [Save to disk]
  • Biological Unit Coordinates (4d0z.pdb1.gz) 170 Kb
  • Biological Unit Coordinates (4d0z.pdb2.gz) 170 Kb
  • Biological Unit Coordinates (4d0z.pdb3.gz) 170 Kb
  • Biological Unit Coordinates (4d0z.pdb4.gz) 170 Kb
  • Biological Unit Coordinates (4d0z.pdb5.gz) 170 Kb
  • Biological Unit Coordinates (4d0z.pdb6.gz) 169 Kb
  • LPC: Ligand-Protein Contacts for 4D0Z
  • CSU: Contacts of Structural Units for 4D0Z
  • Structure Factors (9881 Kb)
  • Retrieve 4D0Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D0Z from S2C, [Save to disk]
  • Re-refined 4d0z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D0Z 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 4D0Z
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4D0Z, from MSDmotif at EBI
  • Fold representative 4d0z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d0z_E] [4d0z_Y] [4d0z_F] [4d0z] [4d0z_B] [4d0z_C] [4d0z_A] [4d0z_D] [4d0z_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4D0Z: [RICIN ] by SMART
  • Other resources with information on 4D0Z
  • Community annotation for 4D0Z at PDBWiki (http://pdbwiki.org)

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