7TUN

Crystal structure analysis of human CKB complex with a covalent compound

• PDB DOI: https://doi.org/10.2210/pdb7TUN/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-03 Released: 2023-02-15 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Crystal Structure Analysis of human CKB complex with a covalent compound

Seo, H.-S., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.46 kDa 
• Atom Count: 5,710 
• Modelled Residue Count: 740 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Creatine kinase B-type	A, B	401	Homo sapiens	Mutation(s): 0  Gene Names: CKB, CKBB EC: 2.7.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12277 (Homo sapiens) Explore P12277  Go to UniProtKB:  P12277
PHAROS:  P12277 GTEx:  ENSG00000166165

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KLU (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2S)-4-(chloroacetyl)-3,4-dihydro-2H-1,4-benzoxazine-2-carboxamide C11 H11 Cl N2 O3 ARXMOGIPJRHYNG-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.24	α = 90
b = 101.24	β = 90
c = 160.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description