8G66 | pdb_00008g66

Structure with SJ3149

• PDB DOI: https://doi.org/10.2210/pdb8G66/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-02-14 Released: 2023-12-13 
• Deposition Author(s): Miller, D.J., Young, S.M., Fischer, M.
• Funding Organization(s): Alexs Lemonade Stand Foundation for Cancer

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structure of ternary complex with molecular glue targeting CK1A for degradation by the CRL4CRBN ubiquitin ligase

Miller, D.J., Young, S.M., Fischer, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 369.13 kDa 
• Atom Count: 21,297 
• Modeled Residue Count: 2,815 
• Deposited Residue Count: 3,254 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A, D	860	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	B, E	426	Homo sapiens	Mutation(s): 0  Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2  Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2 GTEx:  ENSG00000113851

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase I isoform alpha	C, F	341	Homo sapiens	Mutation(s): 0  Gene Names: CSNK1A1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P48729 (Homo sapiens) Explore P48729  Go to UniProtKB:  P48729
PHAROS:  P48729 GTEx:  ENSG00000113712

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YOT (Subject of Investigation/LOI)	H [auth B]	(3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione C20 H16 N4 O4 AJUZTJBGJWQZFW-HNNXBMFYSA-N
ZN	G [auth B], I [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.66	α = 105.49
b = 109.71	β = 94.41
c = 112.34	γ = 100.03

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Miller, D.J., Young, S.M., Fischer, M.

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Funding Organization	Location	Grant Number
Alexs Lemonade Stand Foundation for Cancer	United States	--

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release