4GY5

Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3

Structural Biology Knowledgebase: 4GY5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.255

Literature

Macromolecules
Sequence Display for 4GY5

Classification: Ligase

Total Structure Weight: 115359.77

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase UHRF1 A, B, C, D 241 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: Tudor PHD domain, UNP residues 134-366
Gene Name(s): UHRF1 Gene View ICBP90 NP95 RNF106
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Peptide from Histone H3.3 E, F 17 Homo sapiens Gene Name(s): H3F3A Gene View H3.3A H3F3 PP781 H3F3B Gene View H3.3B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
E, F L-PEPTIDE LINKING C9 H21 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.255
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 145.94 α = 90.00
b = 145.94 β = 90.00
c = 125.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-05
  • Released Date: 2012-11-14
  • Deposition author(s): Cheng, J., Yang, Y., Fang, J., Xiao, J., Zhu, T., Chen, F., Wang, P., Xu, Y.

Revision History

  • 2013-08-07
    Type: Citation | Details: Citation update
  • 2012-11-21
    Type: Entry title | Details: --