6LO2 | pdb_00006lo2

Crystal structure of EED in complex with EZH2 peptide and compound 11#

• PDB DOI: https://doi.org/10.2210/pdb6LO2/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-02 Released: 2021-07-07 
• Deposition Author(s): Zhao, K., Zhao, M., Luo, X., Zhang, H., Chen, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structure of EED in complex with EZH2 peptide and cmpd20

Zhao, K., Zhao, M., Luo, X., Zhang, H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.73 kDa 
• Atom Count: 6,729 
• Modeled Residue Count: 779 
• Deposited Residue Count: 792 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein EED	A, B	367	Homo sapiens	Mutation(s): 0  Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens) Explore O75530  Go to UniProtKB:  O75530
PHAROS:  O75530 GTEx:  ENSG00000074266

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EZH2	C, D	29	Homo sapiens	Mutation(s): 0  EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens) Explore Q15910  Go to UniProtKB:  Q15910
PHAROS:  Q15910 GTEx:  ENSG00000106462

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJU (Subject of Investigation/LOI)	E [auth A], F [auth B]	8-[4-[(dimethylamino)methyl]phenyl]-N-[(2-methoxyphenyl)methyl]-[1,2,4]triazolo[4,3-a]pyridin-5-amine C23 H25 N5 O QKLHJAGJPBYRBR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.31	α = 90
b = 178.18	β = 90
c = 50.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data processing
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Zhao, K., Zhao, M., Luo, X., Zhang, H., Chen, Z.

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary