5VDC Gene Regulation date Apr 01, 2017
title Crystal Structure Of The Human Dpf2 Tandem Phd Finger Domain
authors F.M.Huber, A.M.Davenport, A.Hoelz
compound source
Molecule: Zinc Finger Protein Ubi-D4
Chain: A
Fragment: Dpf2 Tandem Phd Finger Domain (Unp Residues 270-3
Synonym: Apoptosis Response Zinc Finger Protein,Brg1-Associ Factor 45d,Baf45d,D4,Zinc And Double Phd Fingers Family 2,P Requiem;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpf2, Baf45d, Req, Ubid4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 4 2 2
R_factor 0.141 R_Free 0.191
length a length b length c angle alpha angle beta angle gamma
107.500 107.500 53.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand EDO, GOL, ZN enzyme
Primary referenceHistone-binding of DPF2 mediates its repressive role in myeloid differentiation., Huber FM, Greenblatt SM, Davenport AM, Martinez C, Xu Y, Vu LP, Nimer SD, Hoelz A, Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6016-6021. doi:, 10.1073/pnas.1700328114. Epub 2017 May 22. PMID:28533407
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (5vdc.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 5VDC
  • CSU: Contacts of Structural Units for 5VDC
  • Structure Factors (166 Kb)
  • Retrieve 5VDC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VDC from S2C, [Save to disk]
  • Re-refined 5vdc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VDC 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 5VDC
  • 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 5vdc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vdc_A] [5vdc]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VDC
  • Community annotation for 5VDC at PDBWiki (http://pdbwiki.org)

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