5VVT Hydrolase date May 20, 2017
title Structural Investigations Of The Substrate Specificity Of Hu Glcnacase
authors B.Li, J.Jiang, H.Li, C.W.Hu
compound source
Molecule: Protein O-Glcnacase
Chain: A, C
Synonym: Oga,Beta-N-Acetylglucosaminidase,Beta-N- Acetylhexosaminidase,Beta-Hexosaminidase,Meningioma-Express 5,N-Acetyl-Beta-D-Glucosaminidase,N-Acetyl-Beta-Glucosamini Nuclear Cytoplasmic O-Glcnacase And Acetyltransferase,Ncoat
Ec: 3.2.1.169,3.2.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mgea5, Hexc, Kiaa0679, Mea5
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Elk1 Peptide
Chain: B, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.291
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.363 95.793 89.323 90.00 114.51 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand NAG enzyme Hydrolase E.C.3.2.1.169 BRENDA
Primary referenceStructural insights into the substrate binding adaptability and specificity of human O-GlcNAcase., Li B, Li H, Hu CW, Jiang J, Nat Commun. 2017 Sep 22;8(1):666. doi: 10.1038/s41467-017-00865-1. PMID:28939839
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (5vvt.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 5VVT
  • CSU: Contacts of Structural Units for 5VVT
  • Structure Factors (900 Kb)
  • Retrieve 5VVT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VVT from S2C, [Save to disk]
  • View 5VVT 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 5VVT
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vvt_A] [5vvt_C] [5vvt_D] [5vvt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VVT
  • Community annotation for 5VVT at PDBWiki (http://pdbwiki.org)

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