5BX6 | pdb_00005bx6

PKA in complex with a halogenated phthalazinone fragment compound.

• PDB DOI: https://doi.org/10.2210/pdb5BX6/pdb

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


• Deposited: 2015-06-08 Released: 2016-09-14 
• Deposition Author(s): Narayanan, D., Alam, K.A., Engh, R.A.
• Funding Organization(s): FRINAT

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

PKA based studies of ligand interactions with a methionine gatekeeper.

Narayanan, D., Gani, O.A., Alam, K.A., Engh, R.A.

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)

Macromolecule Content 

• Total Structure Weight: 43.65 kDa 
• Atom Count: 3,276 
• Modeled Residue Count: 366 
• Deposited Residue Count: 371 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	351	Homo sapiens	Mutation(s): 0  Gene Names: 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
495	C [auth A]	4-chlorophthalazin-1(2H)-one C8 H5 Cl N2 O QCKGMJDOJRNSMS-UHFFFAOYSA-N
MPD	D [auth A], E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-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: 1.89 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.349	α = 90
b = 75.315	β = 90
c = 80.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Narayanan, D., Alam, K.A., Engh, R.A.

---

Funding Organization	Location	Grant Number
FRINAT	Norway	191303

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary