7AXW

Crystal structure of the cAMP-dependent protein kinase A cocrystallized with 1-aminoisoquinoline and PKI (5-24)

PDB DOI: https://doi.org/10.2210/pdb7AXW/pdb

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

Deposited: 2020-11-10 Released: 2021-11-24
Deposition Author(s): Oebbeke, M., Wienen-Schmidt, B., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Fragment based drug design - Small chemical changes of fragments effecting big changes in binding

Oebbeke, M., Wienen-Schmidt, B., Gerber, H.-D., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 43.48 kDa
Atom Count: 3,255
Modelled Residue Count: 369
Deposited Residue Count: 373
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25321
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	20	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63248
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1SQ (Subject of Investigation/LOI) Query on 1SQ 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]	ISOQUINOLIN-1-AMINE C₉ H₈ N₂ OSILBMSORKFRTB-UHFFFAOYSA-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: 1.69 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.113	α = 90
b = 107.584	β = 90
c = 58.076	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-11-24

Deposition Author(s):

Wienen-Schmidt, B.

Revision History (Full details and data files)

Version 1.0: 2021-11-24
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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.