6BW6 Transferase Antibiotic date Dec 14, 2017
title Human Gpt (Dpagt1) H129 Variant In Complex With Tunicamycin
authors J.Yoo, A.C.Y.Kuk, E.H.Mashalidis, S.Y.Lee
compound source
Molecule: Udp-N-Acetylglucosamine--Dolichyl-Phosphate N- Acetylglucosaminephosphotransferase;
Chain: A, B, C, D
Synonym: Glcnac-1-P Transferase,Gpt,N-Acetylglucosamine-1-P Transferase;
Ec: 2.7.8.15
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpagt1, Dpagt2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: C 1 2 1
R_factor 0.260 R_Free 0.291
crystal
cell
length a length b length c angle alpha angle beta angle gamma
210.615 105.363 148.080 90.00 103.49 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand PGW, TUM enzyme Transferase E.C.2.7.8.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceGlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation., Yoo J, Mashalidis EH, Kuk ACY, Yamamoto K, Kaeser B, Ichikawa S, Lee SY, Nat Struct Mol Biol. 2018 Mar;25(3):217-224. doi: 10.1038/s41594-018-0031-y. Epub, 2018 Feb 19. PMID:29459785
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (458 Kb) [Save to disk]
  • Biological Unit Coordinates (6bw6.pdb1.gz) 226 Kb
  • Biological Unit Coordinates (6bw6.pdb2.gz) 225 Kb
  • LPC: Ligand-Protein Contacts for 6BW6
  • CSU: Contacts of Structural Units for 6BW6
  • Structure Factors (414 Kb)
  • Retrieve 6BW6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6BW6 from S2C, [Save to disk]
  • View 6BW6 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 6BW6
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6bw6_C] [6bw6_B] [6bw6_D] [6bw6_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6BW6
  • Community annotation for 6BW6 at PDBWiki (http://pdbwiki.org)

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