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 1.0 of the entry. See complete history

Literature

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

Local, A.Jung, I.Albuquerque, C.P.Singh, N.Lee, A.Y.Wang, W.Wang, C.Shiau, A.Ge, K.Wang, D.Corbett, K.D.Zhou, H.Ren, B.

To be published.

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
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release