4D0Z	Transferase Peptide	date	Apr 30, 2014
title	Galnac-T2 Crystal Soaked With Udp-5sgalnac, Mea2 And Manganese (Higher 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: Peptide Chain: Y, X 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
Molecule: Polypeptide N-Acetylgalactosaminyltransferase 2 Chain: A, C, B, E, D, F Synonym: Polypeptide Galnac Transferase 2, Galnac-T2, Pp-Ga Protein-Udp Acetylgalactosaminyltransferase 2, Udp-Galnac\ Polypeptide N-Acetylgalactosaminyltransferase 2, Polypepti Galnac-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
symmetry	Space Group: P 21 21 21	R_factor 0.19641 R_Free 0.23377
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 Diffraction	resolution	2.20 Å
ligand	BBK, EDO, HWU, MN	enzyme	Transferase E.C.2.4.1.41 BRENDA
Gene Ontology	Chain Function Process Component F, A, D, C, E, B
Primary reference	Substrate-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] (1019 Kb) [Save to disk] Biological Unit Coordinates (4d0z.pdb1.gz) 176 Kb Biological Unit Coordinates (4d0z.pdb2.gz) 177 Kb Biological Unit Coordinates (4d0z.pdb3.gz) 176 Kb Biological Unit Coordinates (4d0z.pdb4.gz) 176 Kb Biological Unit Coordinates (4d0z.pdb5.gz) 176 Kb Biological Unit Coordinates (4d0z.pdb6.gz) 175 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

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