5SZC

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.193 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of H3K4me1-associated proteins at mammalian enhancers.

Local, A.Huang, H.Albuquerque, C.P.Singh, N.Lee, A.Y.Wang, W.Wang, C.Hsia, J.E.Shiau, A.K.Ge, K.Corbett, K.D.Wang, D.Zhou, H.Ren, B.

(2018) Nat. Genet. 50: 73-82


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger protein DPF3
A
115Homo sapiensMutation(s): 0 
Gene Names: DPF3 (BAF45C, CERD4)
Find proteins for Q92784 (Homo sapiens)
Go to Gene View: DPF3
Go to UniProtKB:  Q92784
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3 tail peptide
H
18Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
H
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
ALY
Query on ALY
H
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 39.321α = 90.00
b = 39.321β = 90.00
c = 147.571γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references, Structure summary