3KKV | pdb_00003kkv

Structure of PKA with a protein Kinase B-selective inhibitor.

PDB DOI: https://doi.org/10.2210/pdb3KKV/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Bos taurus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-06 Released: 2010-12-22
Deposition Author(s): Elkins, P.A., Concha, N.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.225 (Depositor), 0.234 (DCC)
R-Value Work:
0.202 (Depositor), 0.209 (DCC)
R-Value Observed:
0.203 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of PKA with a protein Kinase B-selective inhibitor.

Lin, H., Elkins, P.A., Concha, N.O., Heerding, D., Wang, W., Nidarmarthy, S., Luengo, J.I., Nelson, R., Knick, V.B., Choudhry, A.E.

To be published.

Macromolecule Content

Total Structure Weight: 43.48 kDa
Atom Count: 3,242
Modeled Residue Count: 358
Deposited Residue Count: 370
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	350	Bos taurus	Mutation(s): 0 EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517 Go to UniProtKB: P00517
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00517
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PKI kinase inhibitor	B [auth I]	20	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B99 Query on B99 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]	(2S)-1-{[6-furan-3-yl-5-(3-methyl-2H-indazol-5-yl)pyridin-3-yl]oxy}-3-(1H-indol-3-yl)propan-2-amine C₂₈ H₂₅ N₅ O₂ XONRTPBYDAFIRW-NRFANRHFSA-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: 1.80 Å
R-Value Free: 0.225 (Depositor), 0.234 (DCC)
R-Value Work: 0.202 (Depositor), 0.209 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.411	α = 90
b = 75.996	β = 90
c = 80.39	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-12-10
Changes: Other
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, 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.