7N27 | pdb_00007n27

Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261

• PDB DOI: https://doi.org/10.2210/pdb7N27/pdb

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


• Deposited: 2021-05-28 Released: 2021-07-21 
• Deposition Author(s): Beldar, S., Dong, A., Loppnau, P., Min, J., Arrowsmith, C.H., Edwards, A.M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.262 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261

Beldar, S., Dong, A., Loppnau, P., Min, J., Arrowsmith, C.H., Edwards, A.M., 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: 48.32 kDa 
• Atom Count: 3,279 
• Modeled Residue Count: 377 
• Deposited Residue Count: 378 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Chromodomain Y-like protein	A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	57	Homo sapiens	Mutation(s): 0  Gene Names: CDYL, CDYL1 EC: 4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y232 (Homo sapiens) Explore Q9Y232  Go to UniProtKB:  Q9Y232
PHAROS:  Q9Y232 GTEx:  ENSG00000153046

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
inhibitor UNC6261	B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	M [auth A], N [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX	O [auth D], P [auth F]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PF5	B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	L-PEPTIDE LINKING	C9 H6 F5 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.262 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37N27

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.971	α = 90
b = 76.386	β = 90
c = 80.628	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Beldar, S., Dong, A., Loppnau, P., Min, J., Arrowsmith, C.H., Edwards, A.M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations