Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.75 kDa 
• Atom Count: 3230 
• Modelled Residue Count: 370 
• Deposited Residue Count: 370 
• Unique protein chains: 2

1SMH

Protein kinase A variant complex with completely ordered N-terminal helix

• DOI: 10.2210/pdb1SMH/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE/INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-03-09 Released: 2004-07-06 
• Deposition Author(s): Breitenlechner, C., Engh, R.A., Huber, R., Kinzel, V., Bossemeyer, D., Gassel, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

The Typically Disordered N-Terminus of PKA Can Fold as a Helix and Project the Myristoylation Site into Solution

Breitenlechner, C., Engh, R.A., Huber, R., Kinzel, V., Bossemeyer, D., Gassel, M.

(2004) Biochemistry 43: 7743-7749

• PubMed: 15196017 
• DOI: 10.1021/bi0362525
• Primary Citation of Related Structures:  
  1SMH


• PubMed Abstract: 
  

Protein kinases comprise the major enzyme family critically involved in signal transduction pathways; posttranslational modifications affect their regulation and determine signaling states. The prototype protein kinase A (PKA) possesses an N-terminal alpha-helix (Helix A) that is atypical for kinases and is thus a major distinguishing feature of PKA. Its physiological function may involve myristoylation at the N-terminus and modulation via phosphorylation at serine 10. Here we describe an unusual structure of an unmyristoylated PKA, unphosphorylated at serine 10, with a completely ordered N-terminus. Using standard conditions (e.g., PKI 5-24, ATP site ligand, MEGA-8), a novel 2-fold phosphorylated PKA variant showed the ordered N-terminus in a new crystal packing arrangement. Thus, the critical factor for structuring the N-terminus is apparently the absence of phosphorylation of Ser10. The flexibility of the N-terminus, its myristoylation, and the conformational dependence on the phosphorylation state are consistent with a functional role for myristoylation.

---

Organizational Affiliation: 

Abteilung Strukturforschung, Max-Planck-Institut fuer Biochemie, 82152 Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-Dependent Protein Kinase, alpha-catalytic subunit	A	350	Bos taurus	Mutation(s): 6  Gene Names: PRKACA EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor, alpha form	B	20	N/A	Mutation(s): 0
UniProt
Find proteins for P61926 (Oryctolagus cuniculus) Explore P61926  Go to UniProtKB:  P61926

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG8 (Subject of Investigation/LOI)	H [auth A]	N-OCTANOYL-N-METHYLGLUCAMINE C15 H31 N O6 SBWGZAXBCCNRTM-UHFFFAOYSA-N
BU3	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-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: 2.04 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.78	α = 90
b = 79.431	β = 90
c = 117.82	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-09 
• Released Date: 2004-07-06 
Deposition Author(s): Breitenlechner, C., Engh, R.A., Huber, R., Kinzel, V., Bossemeyer, D., Gassel, M.

Revision History  

• Version 1.0: 2004-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations, Structure summary