5JJZ

Chromo domain of human Chromodomain Protein, Y-Like 2

• PDB DOI: https://doi.org/10.2210/pdb5JJZ/pdb

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


• Deposited: 2016-04-25 Released: 2016-05-25 
• Deposition Author(s): DONG, A., DOMBROVSKI, L., LOPPNAU, P., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., MIN, J., WU, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Starting Model: experimental

Literature

The crystal structure of CDYL2 domain of human CDYL2 protein

WU, H., DONG, A., ZENG, H., ELBAKKOURI, M., BARSYTE, D., VEDADI, M., TATLOCK, J., OWEN, D., BUNNAGE, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., BROWN, P.J.

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.55 kDa 
• Atom Count: 533 
• Modelled Residue Count: 63 
• Deposited Residue Count: 96 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain Y-like protein 2	A	83	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
LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR	B	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10412 (Homo sapiens) Explore P10412  Go to UniProtKB:  P10412
PHAROS:  P10412 GTEx:  ENSG00000168298

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/M35JJZ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.962	α = 90
b = 57.962	β = 90
c = 98.824	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): DONG, A., DOMBROVSKI, L., LOPPNAU, P., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., MIN, J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description