6FRX | pdb_00006frx

PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor

PDB DOI: https://doi.org/10.2210/pdb6FRX/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-16 Released: 2019-03-13
Deposition Author(s): Engh, R.A., Kazi, A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.226 (Depositor), 0.229 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor

Engh, R.A., Kazi, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 43.45 kDa
Atom Count: 3,194
Modeled Residue Count: 354
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	351	Homo sapiens	Mutation(s): 0 Gene Names: PRKACA, PKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612 Go to UniProtKB: P17612
PHAROS: P17612 GTEx: ENSG00000072062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17612
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	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925 Go to UniProtKB: P61925
PHAROS: P61925 GTEx: ENSG00000171033
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E3Z Query on E3Z 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]	~{N}-[3-[(5-chloranyl-2-phenylazanyl-pyrimidin-4-yl)amino]phenyl]prop-2-enamide C₁₉ H₁₆ Cl N₅ O SLKFAKHADUAFCQ-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: 1.88 Å
R-Value Free: 0.226 (Depositor), 0.229 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.743	α = 90
b = 77.784	β = 90
c = 96.484	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, 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.