7BAQ | pdb_00007baq

Crystal structure of the cAMP-dependent protein kinase A cocrystallized with a chiral ligand (S- and E-configuration) and PKI (5-24)

PDB DOI: https://doi.org/10.2210/pdb7BAQ/pdb

Classification: TRANSFERASE
Organism(s): Cricetulus griseus, Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-16 Released: 2022-01-12
Deposition Author(s): Oebbeke, M., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.220 (Depositor), 0.222 (DCC)
R-Value Work:
0.176 (Depositor), 0.178 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of the cAMP-dependent protein kinase A cocrystallized with a chiral ligand (S- and E-configuration) and PKI (5-24)

Oebbeke, M., Koester, H., Brass, S., Gerber, H.-D., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 43.4 kDa
Atom Count: 3,075
Modeled Residue Count: 358
Deposited Residue Count: 371
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	353	Cricetulus griseus	Mutation(s): 0 Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus) Explore P25321 Go to UniProtKB: P25321
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25321
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	18	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P63248 (Mus musculus) Explore P63248 Go to UniProtKB: P63248
IMPC: MGI:104747
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63248
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T82 (Subject of Investigation/LOI) Query on T82 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(S,E)-3-(2-(3-bromo-4-hydroxybenzylidene)hydrazineyl)-2-(3-chlorophenyl)-3-oxopropan-1-aminium C₁₆ H₁₅ Br Cl N₃ O₂ NCMIGNFSEKGWIC-PCQWDSEFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.220 (Depositor), 0.222 (DCC)
R-Value Work: 0.176 (Depositor), 0.178 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.22	α = 90
b = 73.334	β = 90
c = 77.388	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-01-12
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.