7SLW

Complex structure of CDYL2 with an antagonist

• PDB DOI: https://doi.org/10.2210/pdb7SLW/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-10-25 Released: 2021-11-17 
• Deposition Author(s): Beldar, S., Dong, A., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

Literature

Complex structure of CDYL2 with an antagonist

Beldar, S., Dong, A., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B1C1D1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 49.8 kDa 
• Atom Count: 3,155 
• Modelled Residue Count: 376 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain Y-like protein 2	A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	62	Homo sapiens	Mutation(s): 0  Gene Names: CDYL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8U2 (Homo sapiens) Explore Q8N8U2  Go to UniProtKB:  Q8N8U2
PHAROS:  Q8N8U2 GTEx:  ENSG00000166446

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain Y-like protein 2	B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	6	Homo sapiens	Mutation(s): 0  Gene Names: CDYL2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX	N [auth C], O [auth E], P [auth E]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.953	α = 90
b = 81.265	β = 90
c = 122.741	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Beldar, S., Dong, A., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection, Derived calculations