5KL4 Transcription Dna date Jun 23, 2016
title Wilms Tumor Protein (Wt1) Znf2-4 Q369h In Complex With Formy
authors H.Hashimoto, X.Cheng
compound source
Molecule: Wilms Tumor Protein
Chain: A, D
Fragment: Unp Residues 333-420
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: 469008
Expression_system_strain: Bl21 (De3) Ril Codon Plus
Expression_system_vector_type: Pgex-6p-1
Expression_system_plasmid: Pxc1305

Molecule: Dna (5'-D(Apgpcpgptpgpgpgp(5fc)Pgpt)-3
Chain: B, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tpap(5cm)Pgpcpcpcpapcpgpc)-3
Chain: C, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor 0.217 R_Free 0.246
length a length b length c angle alpha angle beta angle gamma
35.766 43.853 54.808 81.95 88.57 88.51
method X-Ray Diffractionresolution 1.78 Å
ligand 5CM, 5FC, CA, EDO, NA, 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] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (5kl4.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (5kl4.pdb2.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 5KL4
  • CSU: Contacts of Structural Units for 5KL4
  • Structure Factors (477 Kb)
  • Retrieve 5KL4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KL4 from S2C, [Save to disk]
  • Re-refined 5kl4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KL4 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 5KL4
  • 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 5kl4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kl4_A] [5kl4_F] [5kl4_D] [5kl4_E] [5kl4_C] [5kl4] [5kl4_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5KL4: [ZnF_C2H2 ] by SMART
  • Other resources with information on 5KL4
  • Community annotation for 5KL4 at PDBWiki (http://pdbwiki.org)

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