8SP6 | pdb_00008sp6

COMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST

• PDB DOI: https://doi.org/10.2210/pdb8SP6/pdb
• Entry: 8SP6 supersedes: 7SLW

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


• Deposited: 2023-05-02 Released: 2024-03-13 
• Deposition Author(s): Song, X., Beldar, S., Dong, A., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

COMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.12 kDa 
• Atom Count: 3,733 
• Modeled Residue Count: 374 
• 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, B, C, D, E, 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
(5R0)FAL(MLZ)(5R5)	G, H, I, J, K, L	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I9A (Subject of Investigation/LOI)	N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L]	(1s,4s)-bicyclo[2.2.1]heptane C7 H12 UMRZSTCPUPJPOJ-KNVOCYPGSA-N
UNX	M [auth D]	UNKNOWN ATOM OR ION X

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5R5	G, H, I, J, K, L	L-PEPTIDE LINKING	C4 H9 N O3		SER
MLZ	G, H, I, J, K, L	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.905	α = 90
b = 88.576	β = 90
c = 113.237	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Song, X., Beldar, S., Dong, A., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
• This entry supersedes: 7SLW

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Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Advisory