2ZKE Ligase date Mar 19, 2008
title Crystal Structure Of The Sra Domain Of Mouse Np95 In Complex Hemi-Methylated Cpg Dna
authors K.Arita, M.Ariyoshi, H.Tochio, Y.Nakamura, M.Shirakawa
compound source
Molecule: E3 Ubiquitin-Protein Ligase Uhrf1
Chain: A
Fragment: Unp Residues 404-613
Synonym: Ubiquitin-Like Phd And Ring Finger Domain-Containi 1, Ubiquitin-Like-Containing Phd And Ring Finger Domains Pr Nuclear Zinc Finger Protein Np95, Nuclear Protein 95;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Uhrf1, Np95
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex

Molecule: Dna (5'-D(Dcpdtpdapdcpdcpdgpdgpdapdtpdt 3');
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Nucleotide Synthesis

Molecule: Dna (5'-D(Dgpdcpdapdapdtpdcp(5cm) Pdgpdgpdtpdapdg)-3');
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Nucleotide Synthesis
symmetry Space Group: P 41 21 2
R_factor 0.219 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.081 59.081 193.971 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 5CM enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceRecognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism., Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M, Nature. 2008 Oct 9;455(7214):818-21. Epub 2008 Sep 3. PMID:18772891
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (2zke.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 2ZKE
  • CSU: Contacts of Structural Units for 2ZKE
  • Likely Quarternary Molecular Structure file(s) for 2ZKE
  • Structure Factors (164 Kb)
  • Retrieve 2ZKE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ZKE from S2C, [Save to disk]
  • Re-refined 2zke structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ZKE 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 2ZKE
  • 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 2ZKE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2zke_D] [2zke_A] [2zke_C] [2zke]
  • SWISS-PROT database: [Q8VDF2]
  • Domain organization of [UHRF1_MOUSE] by SWISSPFAM
  • Domain found in 2ZKE: [SRA ] by SMART
  • Other resources with information on 2ZKE
  • Community annotation for 2ZKE 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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