8XU6 | pdb_00008xu6

Structural Insights into the Tumor Suppressor ZMYND11 Reveal Diverse Recognition Mechanisms

PDB DOI: https://doi.org/10.2210/pdb8XU6/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Homo sapiens
Expression System: prokaryote coculture
Mutation(s): No

Deposited: 2024-01-12 Released: 2025-08-13
Deposition Author(s): Bai, X., Chen, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural Insights into the Tumor Suppressor ZMYND11 Reveal Diverse Recognition Mechanisms

Bai, X., Chen, Z.

To be published.

Macromolecule Content

Total Structure Weight: 6.52 kDa
Atom Count: 447
Modeled Residue Count: 54
Deposited Residue Count: 54
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger MYND domain-containing protein 11	A	54	Homo sapiens	Mutation(s): 0 Gene Names: ZMYND11, BRAM1, BS69
UniProt & NIH Common Fund Data Resources
Find proteins for Q15326 (Homo sapiens) Explore Q15326 Go to UniProtKB: Q15326
PHAROS: Q15326 GTEx: ENSG00000015171
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15326
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.227 (Depositor), 0.227 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.022	α = 90
b = 55.022	β = 90
c = 74.411	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release
Version 1.1: 2025-09-10
Changes: Database references, Derived calculations, Structure summary

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.