8D41 | pdb_00008d41

Crystal structure of the human COPB2 WD-domain in complex with OICR-6254

• PDB DOI: https://doi.org/10.2210/pdb8D41/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-06-01 Released: 2022-07-06 
• Deposition Author(s): Zeng, H., Saraon, P., Dong, A., Hutchinson, A., Seitova, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human COPB2 WD-domain in complex with OICR-6254

Zeng, H., Saraon, P., Dong, A., Hutchinson, A., Seitova, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.7 kDa 
• Atom Count: 5,235 
• Modeled Residue Count: 606 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit beta'	A, B	318	Homo sapiens	Mutation(s): 0  Gene Names: COPB2
UniProt & NIH Common Fund Data Resources
Find proteins for P35606 (Homo sapiens) Explore P35606  Go to UniProtKB:  P35606
PHAROS:  P35606 GTEx:  ENSG00000184432

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q93 (Subject of Investigation/LOI)	C [auth A], F [auth B]	(1R,2R,3S,4S)-3-[4-(4-fluorophenyl)piperazine-1-carbonyl]bicyclo[2.2.1]heptane-2-carboxylic acid C19 H23 F N2 O3 IGLAQRKZPMAAST-UWWPHRKUSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX	E [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38D41

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.015	α = 90
b = 91.149	β = 99.58
c = 58.716	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Zeng, H., Saraon, P., Dong, A., Hutchinson, A., Seitova, A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary