9PKU | pdb_00009pku

Crystal Structure of YEATS domain of human YEATS2 in complex with LS-131 peptide

PDB DOI: https://doi.org/10.2210/pdb9PKU/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-07-14 Released: 2026-01-07
Deposition Author(s): xinyi, Y., sha, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.251 (Depositor), 0.257 (DCC)
R-Value Work:
0.208 (Depositor), 0.217 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Complex-specific chemical probes for interrogating ATAC histone acetyltransferase complex

Sha, L.

To be published.

Macromolecule Content

Total Structure Weight: 34.3 kDa
Atom Count: 2,435
Modeled Residue Count: 275
Deposited Residue Count: 280
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YEATS domain-containing protein 2	A, C	135	Homo sapiens	Mutation(s): 0 Gene Names: YEATS2, KIAA1197
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULM3 (Homo sapiens) Explore Q9ULM3 Go to UniProtKB: Q9ULM3
PHAROS: Q9ULM3 GTEx: ENSG00000163872
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ULM3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LS-131 peptide	B, D	5	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BZ2 (Subject of Investigation/LOI) Query on BZ2 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain Q [auth D] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth D]	H [auth B], Q [auth D]	1-benzofuran-2-carboxylic acid C₉ H₆ O₃ OFFSPAZVIVZPHU-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain Q [auth D] Interactions & Density Focus chain H [auth B] Focus chain Q [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] L [auth C] M [auth C] E [auth A], F [auth A], G [auth A], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	I [auth C], J [auth C], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]