4HAE | pdb_00004hae

Crystal structure of the CDYL2-chromodomain

• PDB DOI: https://doi.org/10.2210/pdb4HAE/pdb

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


• Deposited: 2012-09-26 Released: 2012-10-10 
• Deposition Author(s): Qin, S., Dombrovski, L., Tempel, W., Dong, A., Xu, C., 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: 
  0.251 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the CDYL2-chromodomain

Qin, S., Dombrovski, L., Tempel, W., Dong, A., Xu, C., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 9.93 kDa 
• Atom Count: 573 
• Modeled Residue Count: 66 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain Y-like protein 2	A	81	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.251 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.358	α = 90
b = 60.358	β = 90
c = 89.896	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Qin, S., Dombrovski, L., Tempel, W., Dong, A., Xu, C., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary