3FL2 | pdb_00003fl2

Crystal structure of the ring domain of the E3 ubiquitin-protein ligase UHRF1

• PDB DOI: https://doi.org/10.2210/pdb3FL2/pdb

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


• Deposited: 2008-12-18 Released: 2009-01-20 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.250 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structure of the Ring Domain of the E3 Ubiquitin-Protein Ligase Uhrf1

Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 14.13 kDa 
• Atom Count: 1,009 
• Modeled Residue Count: 116 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A	124	Homo sapiens	Mutation(s): 0  Gene Names: ICBP90, NP95, RNF106, UHRF1 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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.250 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.736	α = 90
b = 46.916	β = 90
c = 48.409	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description