1X3W Hydrolase date May 11, 2005
title Structure Of A Peptide:N-Glycanase-Rad23 Complex
authors J.H.Lee, J.M.Choi, C.Lee, K.J.Yi, Y.Cho
compound source
Molecule: Peptide:N-Glycanase
Chain: A
Fragment: Residues 8-342
Ec: 3.5.1.52
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Uv Excision Repair Protein Rad23
Chain: B
Fragment: Xpc Binding Domain
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
symmetry Space Group: P 31 2 1
R_factor 0.244 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.235 129.235 128.494 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand FRU, GLC, MSE, ZN enzyme Hydrolase E.C.3.5.1.52 BRENDA
related structures by homologous chain: 1X3Z
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins., Lee JH, Choi JM, Lee C, Yi KJ, Cho Y, Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9144-9. Epub 2005 Jun 17. PMID:15964983
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (1x3w.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 1X3W
  • CSU: Contacts of Structural Units for 1X3W
  • Likely Quarternary Molecular Structure file(s) for 1X3W
  • Structure Factors (187 Kb)
  • Retrieve 1X3W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1X3W from S2C, [Save to disk]
  • Re-refined 1x3w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1X3W 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 1X3W
  • 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
  • 3D motif for 1X3W, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1x3w_A] [1x3w] [1x3w_B]
  • SWISS-PROT database: [Q02890] [P32628]
  • Domain organization of [PNG1_YEAST] [RAD23_YEAST] by SWISSPFAM
  • Domains found in 1X3W: [STI1] [TGc ] by SMART
  • Other resources with information on 1X3W
  • Community annotation for 1X3W at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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