6I2D

Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus Griseus in complex with compounds RKp182 and RKp117

PDB DOI: https://doi.org/10.2210/pdb6I2D/pdb
Entry: 6I2D supersedes: 6EMD

Classification: TRANSFERASE
Organism(s): Cricetulus griseus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-11-01 Released: 2019-05-15
Deposition Author(s): Mueller, J.M., Heine, A., Klebe, G.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.222
R-Value Work: 0.188
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage

Mueller, J.M., Kirschner, R., Geyer, A., Klebe, G.

(2019) ACS Omega

DOI: https://doi.org/10.1021/acsomega.8b02364

Macromolecule Content

Total Structure Weight: 43.62 kDa
Atom Count: 2,972
Modelled Residue Count: 361
Deposited Residue Count: 371
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
UPF0418 protein FAM164A	B [auth D]	18	Cricetulus griseus	Mutation(s): 0
UniProt
Find proteins for G3HK48 (Cricetulus griseus) Explore G3HK48 Go to UniProtKB: G3HK48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3HK48
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9LQ (Subject of Investigation/LOI) Query on 9LQ 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]	[2-[(4-isoquinolin-5-ylsulfonyl-1,4-diazepan-1-yl)methyl]phenyl]boronic acid C₂₁ H₂₄ B N₃ O₄ S QFOWOOVTQLNTIX-UHFFFAOYSA-N		Interactions 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: 1.91 Å
R-Value Free: 0.222
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.898	α = 90
b = 83.898	β = 90
c = 60.357	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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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

This entry supersedes: 6EMD

Funding Organization	Location	Grant Number
Other government	Germany	--

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release

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.