Macromolecule Content

Total Structure Weight: 43.06 kDa
Atom Count: 3075
Modelled Residue Count: 361
Deposited Residue Count: 370
Unique protein chains: 2

1APM

2.0 ANGSTROM REFINED CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED WITH A PEPTIDE INHIBITOR AND DETERGENT

PDB DOI: 10.2210/pdb1APM/pdb

Classification: TRANSFERASE(PHOSPHOTRANSFERASE)
Organism(s): Mus musculus
Mutation(s): Yes

Deposited: 1993-01-18 Released: 1993-04-15
Deposition Author(s): Knighton, D.R., Bell, S.M., Zheng, J., Teneyck, L.F., Xuong, N.-H., Taylor, S.S., Sowadski, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

2.0 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent.

Knighton, D.R., Bell, S.M., Zheng, J., Ten Eyck, L.F., Xuong, N.H., Taylor, S.S., Sowadski, J.M.

(1993) Acta Crystallogr D Biol Crystallogr 49: 357-361

PubMed: 15299526 Search on PubMed
DOI: 10.1107/S0907444993000502
Primary Citation of Related Structures:
1APM

PubMed Abstract:

. A mutant (Serl39Ala) of the mouse recombinant catalytic (C) subunit of cAMP-dependent protein kinase was co-crystallized with a peptide inhibitor, PKI(5-24), and MEGA-8 (octanoyl-N-methylglucamide) detergent. This structure was refined using all observed data (30 248 reflections) between 30 and 1.95 A resolution to an R factor of 0.186. R.m.s. deviations of bond lengths and bond angles are 0.013 A and 2.3 degrees, respectively. The final model has 3075 atoms (207 solvent) with a mean B factor of 31.9 A(2). The placement of invariant protein-kinase residues and most C:PKI(5-24) interactions were confirmed, but register errors affecting residues 55-64 and 309-339 were corrected during refinement by shifting the affected sequences toward the C terminus along the previously determined backbone path. New details of C:PKI(5-24) interactions and the Ser338 autophosphorylation site are described, and the acyl group binding site near the catalytic subunit NH(2) terminus is identified.

Related Citations:

Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mg/ATP and Peptide Inhibitor
Zheng, J., Knighton, D.R., Teneyck, L.F., Karlsson, R., Xuong, N.-H., Taylor, S.S., Sowadski, J.M.
(1993) Biochemistry 32: 2154

Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Knighton, D.R., Zheng, J., Teneyck, L.F., Ashford, V.A., Xuong, N.-H., Taylor, S.S., Sowadski, J.M.
(1991) Science 253: 407

Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Knighton, D.R., Zheng, J., Teneyck, L.F., Xuong, N.-H., Taylor, S.S., Sowadski, J.M.
(1991) Science 253: 414

Expression of the Catalytic Subunit of C/AMP-Dependent Protein Kinase in Escherichia Coli
Slice, L.W., Taylor, S.S.
(1989) J Biol Chem 264: 20940

Organizational Affiliation:

Department of Chemistry, University of California, San Diego, La Jolla 92093-0654, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-DEPENDENT PROTEIN KINASE	A [auth E]	350	Mus musculus	Mutation(s): 1 Gene Names: Prkaca, Pkaca EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P05132 (Mus musculus) Explore P05132 Go to UniProtKB: P05132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05132
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE INHIBITOR PKI(5-24)	B [auth I]	20	Mus musculus	Mutation(s): 0 Gene Names: Pkia
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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain C [auth E] MOL2 format, chain C [auth E]	C [auth E]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A [auth E]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A [auth E]	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.186
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.84	α = 90
b = 75.76	β = 90
c = 81.01	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 1993-01-18
Released Date: 1993-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1993-04-15
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Other, Refinement description
Version 1.4: 2019-08-14
Changes: Data collection, Refinement description
Version 1.5: 2021-11-03
Changes: Database references