Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15251.78 
• Atom Count: 1031 
• Residue Count: 133 
• Unique protein chains: 2

5SZB

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

• DOI: 10.2210/pdb5SZB/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2016-08-13 Released: 2017-08-16 
• Deposition Author(s): Singh, N., Local, A., Shiau, A., Ren, B., Corbett, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.2 Å
• R-Value Free: 0.155 
• R-Value Work: 0.138 

Literature

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with 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
Molecule	Chains	Sequence Length	Organism	Details
Zinc finger protein DPF3	A	115	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Histone H3 tail peptide	H	18	Homo sapiens	Mutation(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 Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	H	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.2 Å
• R-Value Free: 0.155 
• R-Value Work: 0.138 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data DOI: 
  10.15785/SBGRID/357 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 39.321	α = 90.00
b = 39.321	β = 90.00
c = 147.571	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-08-13 
• Released Date: 2017-08-16 
• Deposition Author(s): Singh, N., Local, A., Shiau, A., Ren, B., Corbett, K.D.

Revision History 

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