3SHB

Crystal Structure of PHD Domain of UHRF1

• PDB DOI: https://doi.org/10.2210/pdb3SHB/pdb

• Classification: LIGASE/NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-16 Released: 2011-08-24 
• Deposition Author(s): Hu, L., Li, Z., Wang, P., Lin, Y., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2.

Hu, L., Li, Z., Wang, P., Lin, Y., Xu, Y.

(2011) Cell Res 

• PubMed: 21808300 
• DOI: https://doi.org/10.1038/cr.2011.124
• Primary Citation of Related Structures:  
  3SHB

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 10.2 kDa 
• Atom Count: 644 
• Modelled Residue Count: 74 
• Deposited Residue Count: 89 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A	77	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88  Go to UniProtKB:  Q96T88
PHAROS:  Q96T88 GTEx:  ENSG00000276043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 peptide	B	12	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.609	α = 90
b = 36.609	β = 90
c = 219.765	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Hu, L., Li, Z., Wang, P., Lin, Y., Xu, Y.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations