6MM6 | pdb_00006mm6

Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 phosphorylation domain (2699-2904)

PDB DOI: https://doi.org/10.2210/pdb6MM6/pdb

Classification: TRANSFERASE/PROTEIN BINDING
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.261 (Depositor), 0.239 (DCC)
R-Value Work:
0.224 (Depositor)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

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

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

(2019) Mol Cell

Macromolecule Content

Total Structure Weight: 129.1 kDa
Atom Count: 9,029
Modeled Residue Count: 1,041
Deposited Residue Count: 1,096
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A [auth C], B [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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05132
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 2	C [auth F], D	209	Mus musculus	Mutation(s): 1 Gene Names: Ryr2
UniProt & NIH Common Fund Data Resources
Find proteins for E9Q401 (Mus musculus) Explore E9Q401 Go to UniProtKB: E9Q401
IMPC: MGI:99685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E9Q401
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain F [auth C] MOL2 format, chain I [auth E] MOL2 format, chain F [auth C] mmCIF format, chain I [auth E] mmCIF format, chain F [auth C]	F [auth C], I [auth E]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain F [auth C] Focus chain I [auth E] Interactions & Density Focus chain F [auth C] Focus chain I [auth E]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth E] MOL2 format, chain J [auth E] mmCIF format, chain J [auth E]	J [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth E] Interactions & Density Focus chain J [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain H [auth C] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain H [auth C] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain H [auth C]	H [auth C], K [auth E], L [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth C] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain H [auth C] Focus chain K [auth E] Focus chain L [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.261 (Depositor), 0.239 (DCC)
R-Value Work: 0.224 (Depositor)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.451	α = 105.51
b = 74.944	β = 90.14
c = 88.69	γ = 94.39

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-08

Deposition Author(s):

van Petegem, F.

Haji-Ghassemi, O.

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

Revision History (Full details and data files)

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, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary