3QBY Protein Binding date Jan 14, 2011
title Crystal Structure Of The Pwwp Domain Of Human Hepatoma-Deriv Factor 2
authors H.Zeng, W.Tempel, M.F.Amaya, M.A.Adams-Cioaba, F.Mackenzie, C.Bou J.Weigelt, C.H.Arrowsmith, A.M.Edwards, J.Min, H.Wu, Structural Consortium (Sgc)
compound source
Molecule: Hepatoma-Derived Growth Factor-Related Protein 2
Chain: A, B, C
Fragment: Unp Residues 1-93
Synonym: Hrp-2, Hepatoma-Derived Growth Factor 2, Hdgf-2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hdgfrp2, Hdgf2, Unq785pro1604
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) V2r-Prare
Expression_system_plasmid: Pet28-Mhl

Molecule: H4k20me3 Histone H4 Peptide
Chain: H
Engineered: Yes

Synthetic: Yes
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.527 41.681 156.749 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand M3L, SO4, UNX enzyme
Primary referenceStructural and Histone Binding Ability Characterizations of Human PWWP Domains., Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J, PLoS One. 2011;6(6):e18919. Epub 2011 Jun 20. PMID:21720545
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (3qby.pdb1.gz) 86 Kb
  • LPC: Ligand-Protein Contacts for 3QBY
  • CSU: Contacts of Structural Units for 3QBY
  • Structure Factors (290 Kb)
  • Retrieve 3QBY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QBY from S2C, [Save to disk]
  • Re-refined 3qby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QBY 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 3QBY
  • 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
  • 3D motif for 3QBY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qby_A] [3qby] [3qby_H] [3qby_C] [3qby_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3QBY: [PWWP ] by SMART
  • Other resources with information on 3QBY
  • Community annotation for 3QBY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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