8FEC

Structure of J-PKAc chimera complexed with Aplithianine derivative

• PDB DOI: https://doi.org/10.2210/pdb8FEC/pdb

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


• Deposited: 2022-12-06 Released: 2023-10-18 
• Deposition Author(s): Du, L., Wilson, B.A.P., Li, N., Martinez Fiesco, J.A., Dalilian, M., Wang, D., Smith, E.A., Wamiru, A., Goncharova, E.I., Zhang, P., O'Keefe, B.R.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.287 
• R-Value Work: 0.208 
• R-Value Observed: 0.214 

Literature

Structures of J-PKAc chimera complexed with Aplithianine and derivatives

Du, L., Wilson, B.A.P., Li, N., Martinez Fiesco, J.A., Dalilian, M., Wang, D., Smith, E.A., Wamiru, A., Goncharova, E.I., Zhang, P., O'Keefe, B.R.

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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.31 kDa 
• Atom Count: 7,064 
• Modelled Residue Count: 848 
• Deposited Residue Count: 850 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha	A	405	Homo sapiens	Mutation(s): 0  Gene Names: DNAJB1, DNAJ1, HDJ1, HSPF1, PRKACA, PKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612  Go to UniProtKB:  P17612
PHAROS:  P17612 GTEx:  ENSG00000072062
Find proteins for P25685 (Homo sapiens) Explore P25685  Go to UniProtKB:  P25685
PHAROS:  P25685 GTEx:  ENSG00000132002
UniProt Groups	P17612P25685

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B [auth I], D [auth J]	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925  Go to UniProtKB:  P61925
PHAROS:  P61925 GTEx:  ENSG00000171033

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha	C [auth B]	405	Homo sapiens	Mutation(s): 0  Gene Names: DNAJB1, DNAJ1, HDJ1, HSPF1, PRKACA, PKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612  Go to UniProtKB:  P17612
PHAROS:  P17612 GTEx:  ENSG00000072062
Find proteins for P25685 (Homo sapiens) Explore P25685  Go to UniProtKB:  P25685
PHAROS:  P25685 GTEx:  ENSG00000132002
UniProt Groups	P17612P25685

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XU0 (Subject of Investigation/LOI)	E [auth A], F [auth B]	6-[(6P)-6-(4-bromo-1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-7H-purine C13 H12 Br N7 S PKNMXSKJZWOKSJ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.287 
• R-Value Work: 0.208 
• R-Value Observed: 0.214 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.64	α = 88.95
b = 59.1	β = 86.14
c = 91.008	γ = 89.86

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Du, L., Wilson, B.A.P., Li, N., Martinez Fiesco, J.A., Dalilian, M., Wang, D., Smith, E.A., Wamiru, A., Goncharova, E.I., Zhang, P., O'Keefe, B.R.

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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: 2023-10-18
  Type: Initial release