5KL3 Transcription Dna date Jun 23, 2016
title Wilms Tumor Protein (Wt1) Znf2-4 Q369h In Complex With Dna
authors H.Hashimoto, X.Cheng
compound source
Molecule: Wilms Tumor Protein
Chain: A
Synonym: Wt33
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Variant: -Kts
Gene: Wt1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Ril-Codon Plus
Expression_system_vector_type: Pgex-6p-1
Expression_system_plasmid: Pxc1305

Molecule: Dna (5'-D(Apgpcpgptpgpgpgpapgpt)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.162 R_Free 0.182
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.223 66.069 35.646 90.00 91.75 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand EDO, ZN enzyme
Primary referenceDenys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications., Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X, Nucleic Acids Res. 2016 Sep 4. pii: gkw766. PMID:27596598
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (5kl3.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 5KL3
  • CSU: Contacts of Structural Units for 5KL3
  • Structure Factors (441 Kb)
  • Retrieve 5KL3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KL3 from S2C, [Save to disk]
  • Re-refined 5kl3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KL3 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 5KL3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5kl3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kl3] [5kl3_C] [5kl3_B] [5kl3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5KL3: [ZnF_C2H2 ] by SMART
  • Other resources with information on 5KL3
  • Community annotation for 5KL3 at PDBWiki (http://pdbwiki.org)

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