8EBK | pdb_00008ebk

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free:
0.187 (Depositor), 0.192 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

Literature

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

Seo, H.-S., Dhe-Paganon, S.

To be published.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7ZUW7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
0EH Query on 0EH	B	D-PEPTIDE LINKING	C₁₀ H₂₁ N O₂		--
MK8 Query on 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 (Depositor), 0.192 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)
R-Value Observed: 0.165 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Dhe-Paganon, S.

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

Revision History (Full details and data files)

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
Version 2.2: 2026-03-04
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.