5AJP Transferase date Feb 26, 2015
title Crystal Structure Of The Active Form Of Galnac-T2 In Complex With Udp And The Glycopeptide Muc5ac-13
authors E.Lira-Navarrete, M.Delasrivas, I.Companon, M.C.Pallares, Y.Kong J.Iglesias-Fernandez, G.J.L.Bernardes, J.M.Peregrina, C.Rovira P.Bernado, P.Bruscolini, H.Clausen, A.Lostao, F.Corzana, R.Hurtado-Guerrero
compound source
Molecule: Polypeptide N-Acetylgalactosaminyltransferase 2
Chain: A
Synonym: Polypeptide Galnac Transferase 2, Galnac-T2, Pp-Ga Protein-Udp Acetylgalactosaminyltransferase 2,
Udp-Galnac\: Polypeptide N-Acetylgalactosaminyltransferase Polypeptide N-Acetylgalactosaminyltransferase 2 Soluble Fo
Ec: 2.4.1.41
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Smd1168
Expression_system_vector: Ppiczalphaa

Molecule: Mucin
Chain: B
Fragment: Residues 65-79
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Komagataella Pastoris
Expression_system_taxid: 4922
Expression_system_strain: Smd1168
Expression_system_vector: Ppiczalphaa
symmetry Space Group: I 41
R_factor 0.15598 R_Free 0.18558
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.266 87.266 178.590 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand A2G, MN, SO4, UDP enzyme Transferase E.C.2.4.1.41 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation., Lira-Navarrete E, de Las Rivas M, Companon I, Pallares MC, Kong Y, Iglesias-Fernandez J, Bernardes GJ, Peregrina JM, Rovira C, Bernado P, Bruscolini P, Clausen H, Lostao A, Corzana F, Hurtado-Guerrero R, Nat Commun. 2015 May 5;6:6937. doi: 10.1038/ncomms7937. PMID:25939779
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (187 Kb) [Save to disk]
  • Biological Unit Coordinates (5ajp.pdb1.gz) 180 Kb
  • LPC: Ligand-Protein Contacts for 5AJP
  • CSU: Contacts of Structural Units for 5AJP
  • Structure Factors (4453 Kb)
  • Retrieve 5AJP in mmCIF format [Save to disk]
  • Re-refined 5ajp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5AJP 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 5AJP
  • 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 5AJP, from MSDmotif at EBI
  • Fold representative 5ajp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ajp] [5ajp_A] [5ajp_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5AJP: [RICIN ] by SMART
  • Other resources with information on 5AJP
  • Community annotation for 5AJP at PDBWiki (http://pdbwiki.org)

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