5EDN Transcription date Oct 21, 2015
title Structure Of Hoxb13-Dna(Tcg) Complex
authors E.Morgunova, Y.Yin, A.Jolma, A.Popov, J.Taipale
compound source
Molecule: Homeobox Protein Hox-B13
Chain: A, B, G, J
Fragment: Unp Residues 209-284
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hoxb13
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petg20a

Molecule: Dna (5'- D(Pgptptpgptpgptptptptpapcpgpapgpgptpcpc
Chain: C, D, H, K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Pgpgpapcpcptpcpgptpapapapapcpapcpapapc
Chain: E, F, I, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 2 2 21
R_factor 0.216 R_Free 0.281
length a length b length c angle alpha angle beta angle gamma
52.618 52.522 389.331 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand TRS enzyme
A, J, G, B

Primary referenceTwo distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima., Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J, Elife. 2018 Apr 11;7. pii: 32963. doi: 10.7554/eLife.32963. PMID:29638214
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (5edn.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (5edn.pdb2.gz) 27 Kb
  • Biological Unit Coordinates (5edn.pdb3.gz) 27 Kb
  • Biological Unit Coordinates (5edn.pdb4.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 5EDN
  • CSU: Contacts of Structural Units for 5EDN
  • Structure Factors (1432 Kb)
  • Retrieve 5EDN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EDN from S2C, [Save to disk]
  • Re-refined 5edn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EDN 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 5EDN
  • 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 5edn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5edn_G] [5edn_F] [5edn_I] [5edn] [5edn_A] [5edn_B] [5edn_L] [5edn_J] [5edn_E] [5edn_C] [5edn_H] [5edn_D] [5edn_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EDN: [HOX ] by SMART
  • Other resources with information on 5EDN
  • Community annotation for 5EDN at PDBWiki (http://pdbwiki.org)

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