6MM5 | pdb_00006mm5

Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810)

• PDB DOI: https://doi.org/10.2210/pdb6MM5/pdb

• Classification: TRANSFERASE/PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-29 Released: 2019-05-08 
• Deposition Author(s): van Petegem, F., Haji-Ghassemi, O.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.227 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810)

Haji-Ghassemi, O., Yuchi, Z., van Petegem, F.

(2019) Mol Cell 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 41.69 kDa 
• Atom Count: 3,147 
• Modeled Residue Count: 350 
• Deposited Residue Count: 351 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A [auth E]	339	Mus musculus	Mutation(s): 0  Gene Names: Prkaca, Pkaca EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus) Explore P05132  Go to UniProtKB:  P05132

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 2	B [auth C]	12	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for E9Q401 (Mus musculus) Explore E9Q401  Go to UniProtKB:  E9Q401
IMPC:  MGI:99685

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth E]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
EDO	E [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.227 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.861	α = 90
b = 74.881	β = 90
c = 98.561	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): van Petegem, F., Haji-Ghassemi, O.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT 153305

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary