8EBK

Crystal Structure Analysis of xHDMX in complex with the stapled peptide PROTAC analog

• PDB DOI: https://doi.org/10.2210/pdb8EBK/pdb

• Classification: APOPTOSIS
• Organism(s): Danio rerio, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-08-31 Released: 2023-10-04 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.187 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Crystal Structure Analysis of xHDMX in complex with the stapled peptide PROTAC analog

Seo, H.-S., Dhe-Paganon, S.

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

Macromolecule Content

• Total Structure Weight: 17.12 kDa 
• Atom Count: 1,007 
• Modelled Residue Count: 102 
• Deposited Residue Count: 147 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HDMX	A	131	Danio rerio	Mutation(s): 0
UniProt
Find proteins for Q7ZUW7 (Danio rerio) Explore Q7ZUW7  Go to UniProtKB:  Q7ZUW7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-LEU-THR-PHE-0EH-GLU-TYR-TRP-ALA-GLN-LEU-MK8-SER-ALA-ALA	B	16	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	B	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.187 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.52	α = 90
b = 108.4	β = 90
c = 30.73	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-06
  Changes: Structure summary