5EGB Transcription Dna date Oct 26, 2015
title Human Prdm9 Allele-A Znf Domain With Associated Recombinatio Dna Sequence II
authors A.Patel, J.R.Horton, G.G.Wilson, X.Zhang, X.Cheng
compound source
Molecule: Dna (5'- D(Apcpcpapcpgptpgpgpcptpapgpgpgpapgpgpcp 3');
Chain: C
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'- D(Tpapgpgpcpcptpcpcpcptpapgpcpcpapcpgptp 3');
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Histone-Lysine N-Methyltransferase Prdm9
Chain: A
Fragment: Znf8-12 (Unp Residues 717-858)
Synonym: Pr Domain Zinc Finger Protein 9,Pr Domain-Containi 9;
Ec: 2.1.1.43
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Variant: Allele-A
Gene: Prdm9, Pfm6
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Codon-Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-1
symmetry Space Group: P 1 21 1
R_factor 0.193 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.575 79.221 68.415 90.00 95.42 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand ZN enzyme Transferase E.C.2.1.1.43 BRENDA
Primary referenceStructural basis for human PRDM9 action at recombination hot spots., Patel A, Horton JR, Wilson GG, Zhang X, Cheng X, Genes Dev. 2016 Feb 1;30(3):257-65. doi: 10.1101/gad.274928.115. PMID:26833727
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (5egb.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 5EGB
  • CSU: Contacts of Structural Units for 5EGB
  • Structure Factors (212 Kb)
  • Retrieve 5EGB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EGB from S2C, [Save to disk]
  • Re-refined 5egb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5EGB 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 5EGB
  • 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: [5egb_C] [5egb] [5egb_A] [5egb_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EGB: [ZnF_C2H2 ] by SMART
    • Other resources with information on 5EGB
  • Community annotation for 5EGB at PDBWiki (http://pdbwiki.org)

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