4ZBN Immune System Dna date Apr 15, 2015
title Non-Helical Dna Triplex Forms A Unique Aptamer Scaffold For Affinity Recognition Of Nerve Growth Factor
authors D.R.Davies, T.E.Edwards
compound source
Molecule: Dna (28-Mer)
Chain: D, E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Beta-Nerve Growth Factor
Chain: A, B
Synonym: Beta-Ngf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ngf, Ngfb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.202 R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
109.201 60.708 68.589 90.00 95.57 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand DUZ, EPE enzyme
A, B

Primary referenceNon-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor., Jarvis TC, Davies DR, Hisaminato A, Resnicow DI, Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H, Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y, Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider DJ, Janjic N, Structure. 2015 May 13. pii: S0969-2126(15)00145-8. doi:, 10.1016/j.str.2015.03.027. PMID:26027732
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (4zbn.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 4ZBN
  • CSU: Contacts of Structural Units for 4ZBN
  • Structure Factors (308 Kb)
  • Retrieve 4ZBN in mmCIF format [Save to disk]
  • Re-refined 4zbn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ZBN 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 4ZBN
  • 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
  • 3D motif for 4ZBN, from MSDmotif at EBI
  • Fold representative 4zbn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4zbn_B] [4zbn_A] [4zbn_E] [4zbn_D] [4zbn]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4ZBN: [NGF ] by SMART
  • Other resources with information on 4ZBN
  • Community annotation for 4ZBN at PDBWiki (http://pdbwiki.org)

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