5R69 | pdb_00005r69

XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e

• PDB DOI: https://doi.org/10.2210/pdb5R69/pdb
• Deposition Group: G_1002134 (changed state) | Explore  G_1002134  

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-29 Released: 2020-12-30 
• Deposition Author(s): Raux, B., Krojer, T., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Huber, K.V.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.248 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

XChem group deposition

Raux, B., Krojer, T., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Huber, K.V.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 43.21 kDa 
• Atom Count: 2,372 
• Modeled Residue Count: 265 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YEATS domain-containing protein 4	A [auth B], B [auth A]	181	Homo sapiens	Mutation(s): 0  Gene Names: YEATS4, GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens) Explore O95619  Go to UniProtKB:  O95619
PHAROS:  O95619 GTEx:  ENSG00000127337

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZHA (Subject of Investigation/LOI)	D [auth B], G [auth A]	~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide C12 H13 N O2 WEBCZGJWXXPNHB-UHFFFAOYSA-N
EDO	C [auth B], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.248 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.6	α = 67.58
b = 47.44	β = 68.56
c = 58.45	γ = 69.02

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Raux, B., Krojer, T., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Huber, K.V.M.

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary