5EH2 Transcription Dna date Oct 27, 2015
title Human Prdm9 Allele-A Znf Domain With Associated Recombinatio Dna Sequence III
authors A.Patel, J.R.Horton, G.G.Wilson, X.Zhang, X.Cheng
compound source
Molecule: Dna (5'- D(Apcpapcpgptpgpgpcptpapgpgpgpapgpgpcpcp 3');
Chain: C, A
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'- D(Tpgpapgpgpcpcptpcpcpcptpapgpcpcpapcpgp 3');
Chain: D, B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Histone-Lysine N-Methyltransferase Prdm9
Chain: E, F
Fragment: Znf8-12 (Unp Residues 717-858)
Synonym: Pr Domain Zinc Finger Protein 9,Pr Domain-Containi 9;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Variant: Alelle-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
R_factor 0.201 R_Free 0.231
length a length b length c angle alpha angle beta angle gamma
45.208 57.756 76.206 90.15 75.30 83.30
method X-Ray Diffractionresolution 2.05 Å
ligand ZN enzyme Transferase E.C. 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] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (5eh2.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (5eh2.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 5EH2
  • CSU: Contacts of Structural Units for 5EH2
  • Structure Factors (408 Kb)
  • Retrieve 5EH2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EH2 from S2C, [Save to disk]
  • Re-refined 5eh2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EH2 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 5EH2
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1w5eh2, region H:232-354 [Jmol] [rasmolscript] [script source]
  • Fold representative 5eh2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5eh2_C] [5eh2_B] [5eh2_D] [5eh2_A] [5eh2_E] [5eh2_F] [5eh2]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EH2: [ZnF_C2H2 ] by SMART
  • Other resources with information on 5EH2
  • Community annotation for 5EH2 at PDBWiki (http://pdbwiki.org)

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