Macromolecule Content

Total Structure Weight: 43.12 kDa
Atom Count: 3,225
Modelled Residue Count: 356
Deposited Residue Count: 370
Unique protein chains: 2

3DND

cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24

PDB DOI: 10.2210/pdb3DND/pdb

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

Deposited: 2008-07-02 Released: 2009-06-23
Deposition Author(s): Schiffer, A., Wendt, K.U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.253
R-Value Work: 0.189
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystallography-independent determination of ligand binding modes

Orts, J., Tuma, J., Reese, M., Grimm, S.K., Monecke, P., Bartoschek, S., Schiffer, A., Wendt, K.U., Griesinger, C., Carlomagno, T.

(2008) Angew Chem Int Ed Engl 47: 7736-7740

PubMed: 18767090 Search on PubMed
DOI: 10.1002/anie.200801792
Primary Citation of Related Structures:
3DND, 3DNE

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	350	Bos taurus	Mutation(s): 0 Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517 Go to UniProtKB: P00517
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00517
Protein Feature View 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 [auth I]	20	N/A	Mutation(s): 0
UniProt
Find proteins for P61926 (Oryctolagus cuniculus) Explore P61926 Go to UniProtKB: P61926
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61926
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LL2 Query on LL2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5-benzyl-1,3-thiazol-2-amine C₁₀ H₁₀ N₂ S FJIMLXBJUVLMMN-UHFFFAOYSA-N		Ligand Interaction

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

Binding Affinity Annotations
ID	Source	Binding Affinity
LL2	PDBBind: 3DND	Ki: 1.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.253
R-Value Work: 0.189
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.045	α = 90
b = 77.649	β = 90
c = 80.088	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-10-09
Changes: Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.