PDB-6y89: Crystal structure of the cAMP-dependent protein kinase A cocrysta...

ID or keywords:

Entry

Database: PDB / ID: 6y89

Title

Crystal structure of the cAMP-dependent protein kinase A cocrystallized with Methyl 5-isoquinolinecarboxylate and PKI (5-24)

Components

(cAMP-dependent protein kinase ...) x 2

Keywords

TRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase

Function / homology

Function and homology information

regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cellular response to heat / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function

Biological species

Cricetulus griseus (Chinese hamster)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Oebbeke, M. / Gerber, H.-D. / Heine, A. / Klebe, G.

Citation

Journal: To Be Published
Title: Fragment based drug design - Small chemical changes of fragments effecting big changes in binding
Authors: Oebbeke, M. / Wienen-Schmidt, B. / Gerber, H.-D. / Heine, A. / Klebe, G.

History

Deposition	Mar 4, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 31, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6y89.cif.gz	199.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6y89.ent.gz	128.7 KB	Display	PDB format
PDBx/mmJSON format	6y89.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6y89_validation.pdf.gz	960.6 KB	Display	wwPDB validaton report
Full document	6y89_full_validation.pdf.gz	961 KB	Display
Data in XML	6y89_validation.xml.gz	19.1 KB	Display
Data in CIF	6y89_validation.cif.gz	28.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y8/6y89 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y89	HTTPS FTP

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Related structure data

Related structure data	6f14SC 6y05C 6y0bC 6y2oC 6y2uC 6yotC 6youC 7axtC 7axvC 7axwC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3dne-d 1fmo-d 4dg2-d 5n23-d 6esa-d 2gnf-d 3mvj-3 4dg0-d 4dfz-d 5ol3-d 2qur-d 1apm-d 5uzk-d 4ujb-d 3ama-d 6ynt-d 4ij9-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (8) #183 - Mar 2015 Phototropin similarity (8) #196 - Apr 2016 Lead Poisoning similarity (3) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: cAMP-dependent protein kinase catalytic subunit alpha

B: cAMP-dependent protein kinase inhibitor alpha

hetero molecules

43.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.124, 78.990, 88.373
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AB

#1: Protein	cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha Mass: 41033.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide	cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248

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Non-polymers , 5 types, 375 molecules

#3: Chemical	ChemComp-OGB / methyl isoquinoline-5-carboxylate Mass: 187.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₉NO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Chemical	ChemComp-MOH / METHANOL Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₄O
#6: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.91 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 30 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8, 15 mM methyl 5-isoquinolinecarboxylate, 0.5 mM PKI (5-24) and 18-23 % methanol (v/v)0.004 mL ...Details: 30 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8, 15 mM methyl 5-isoquinolinecarboxylate, 0.5 mM PKI (5-24) and 18-23 % methanol (v/v)0.004 mL drop volume, 1.0 mL reservoir volume

Crystal

Density Matthews: 2.73 Å³/Da / Density % sol: 54.91 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 30 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8, 15 mM methyl 5-isoquinolinecarboxylate, 0.5 mM PKI (5-24) and 18-23 % methanol (v/v)0.004 mL ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.559→44.19 Å / Num. obs: 64253 / % possible obs: 99.4 % / Redundancy: 4.8 % / B_iso Wilson estimate: 15.43 Å² / R_sym value: 0.069 / Net I/σ(I): 13.44
Reflection shell	Resolution: 1.56→1.65 Å / Mean I/σ(I) obs: 2.64 / Num. unique obs: 10188 / R_sym value: 0.499

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHASER		phasing
Coot	0.89	model building
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6F14

6f14

Resolution: 1.56→44.19 Å / SU ML: 0.1449 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2782

	R_factor	Num. reflection	% reflection
R_free	0.1916	3213	5 %
R_work	0.1684	-	-
obs	0.1695	64250	99.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 19.49 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→44.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2836	0	42	369	3247

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0056	3015
X-RAY DIFFRACTION	f_angle_d	0.8166	4094
X-RAY DIFFRACTION	f_chiral_restr	0.0511	440
X-RAY DIFFRACTION	f_plane_restr	0.0057	549
X-RAY DIFFRACTION	f_dihedral_angle_d	16.3332	1783

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.56-1.58	0.2494	135	0.2189	2568	X-RAY DIFFRACTION	97.83
1.58-1.61	0.2171	139	0.1985	2630	X-RAY DIFFRACTION	99.89
1.61-1.63	0.1903	136	0.1883	2595	X-RAY DIFFRACTION	99.35
1.63-1.66	0.208	138	0.1854	2626	X-RAY DIFFRACTION	98.89
1.66-1.69	0.2346	138	0.1827	2610	X-RAY DIFFRACTION	98.88
1.69-1.72	0.2046	138	0.1744	2625	X-RAY DIFFRACTION	99.57
1.72-1.76	0.203	138	0.166	2630	X-RAY DIFFRACTION	99.6
1.76-1.8	0.1896	139	0.1646	2637	X-RAY DIFFRACTION	99.57
1.8-1.84	0.1912	139	0.1651	2635	X-RAY DIFFRACTION	99.68
1.84-1.89	0.1876	139	0.1568	2652	X-RAY DIFFRACTION	99.82
1.89-1.94	0.2039	139	0.1611	2638	X-RAY DIFFRACTION	99.93
1.94-1.99	0.1994	137	0.1674	2607	X-RAY DIFFRACTION	98.78
1.99-2.06	0.1933	140	0.1646	2655	X-RAY DIFFRACTION	99.5
2.06-2.13	0.1837	140	0.1565	2657	X-RAY DIFFRACTION	99.47
2.13-2.22	0.1793	140	0.1587	2658	X-RAY DIFFRACTION	99.82
2.22-2.32	0.192	140	0.1607	2657	X-RAY DIFFRACTION	99.82
2.32-2.44	0.243	139	0.1742	2646	X-RAY DIFFRACTION	99.61
2.44-2.59	0.1884	140	0.1729	2659	X-RAY DIFFRACTION	98.83
2.59-2.79	0.2058	141	0.175	2678	X-RAY DIFFRACTION	99.75
2.79-3.07	0.1676	142	0.1679	2696	X-RAY DIFFRACTION	99.86
3.07-3.52	0.1641	142	0.1628	2709	X-RAY DIFFRACTION	99.72
3.52-4.43	0.1831	144	0.1503	2728	X-RAY DIFFRACTION	99.1
4.43-44.19	0.1916	150	0.1846	2841	X-RAY DIFFRACTION	98.94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0466121755988	0.0249724173096	-0.0303942661422	0.0134718893603	-0.0115792815421	0.0389737976707	-0.0591460088314	-0.070548395889	0.0846447219041	0.124223334381	0.00883430169899	-0.100439608772	-0.200397846079	-0.0953441448002	-2.42196524085E-5	0.140732302027	0.00737568093046	-0.00316653315673	0.135736774394	-0.00713688590323	0.151439360796	12.0363863952	-5.01082053522	-3.38323634519
2	0.277095854255	0.00431667109754	0.0523546887377	0.369450138246	-0.170977638647	0.247047428843	0.0178843314404	0.226235606884	-0.0643810166652	-0.186481152115	0.0447197132377	-0.0981759328452	0.0521025026777	0.0649147475739	0.000111618571364	0.133543755723	0.00570282863451	0.00613324215207	0.198016783177	-0.0279511776768	0.202147272931	26.711986482	-22.400738569	-20.1375899736
3	0.722134684315	-0.214380124374	0.0803971982591	0.488180011347	0.0264760832858	0.015169846137	0.0303531661032	0.176173955685	-0.0203739505123	-0.0910699297376	-0.062520756001	-0.0706771405547	-0.0126844340324	0.0332568130439	-0.00519263663658	0.128839215145	0.0083677222279	0.0188202217713	0.141468077136	0.00147917348576	0.102905600848	17.8934948208	-15.277922481	-21.5554824774
4	0.179690111281	0.0808498281515	0.0154467400726	0.228128826662	0.0527727099125	0.0107088956651	0.0712766710954	0.0578091934251	-0.0461276710008	0.0223096458579	-0.0538549715657	-0.0646421743153	0.0306478026671	0.0503500103029	0.0465651832853	0.110646246487	0.0136453356898	0.0125136587297	0.11449249818	-0.00897873919448	0.120467160735	10.6804909352	-29.3646475988	-15.6457087059
5	0.511820457409	0.135691294048	0.0408927810538	0.0887766862231	0.109216413253	0.184962404541	-0.0204259020314	0.0345825807786	-0.0031494529332	-0.0488412969091	0.0109354169004	-0.00406986924993	0.00225377282458	-0.0195971398623	-0.000184848347355	0.11097573266	0.00561200501567	-0.00241548659058	0.090038801712	0.00334919784064	0.0938748951567	4.70723509509	-17.5060016201	-12.5270325723
6	0.353562621487	0.21223843891	-0.00359138938647	0.707471666537	-0.0927950819884	0.346615139406	-0.00656237206274	0.0721563312731	0.0283658402159	-0.090269459795	0.0118968002754	0.116799389656	0.038646210955	-0.083082329076	0.000933181852032	0.111359654904	0.00181217087856	-0.00630908050081	0.116464396539	0.0025615368625	0.0985031222657	-8.92848857699	-22.0193582514	-17.565307584
7	0.818441294428	0.323436500542	-0.0548151962736	0.190968585071	0.111397257725	0.637920745548	0.0344679270426	-0.179779112732	0.111540248535	0.0149631106728	-0.0251949484713	0.0109840622035	0.0270864872927	-0.0885258417068	0.0216183418287	0.102287624325	-0.00376940837549	0.0138099807496	0.0830060237154	-0.00958753069181	0.106163651675	-3.01388469485	-19.1184788733	-2.62820118417
8	0.859543071143	-0.137151912264	0.083484333823	0.153055559169	0.0572680311297	0.161128712005	-0.0203529649544	0.313587566176	-0.207848857399	-0.246592564035	-0.0159703790558	-0.110202853981	0.118334204639	-0.0168471222968	0.0419101285659	0.213893129163	0.0201912448532	0.0577885576175	0.230722886827	-0.0314500115646	0.192620237227	21.6047625406	-24.5620284338	-25.3969796438
9	0.0559648905096	0.0170567535661	-0.0406320092883	0.0340475769597	0.0105948590802	0.0464021582083	-0.00249222004786	-0.271595088527	0.0873444825129	0.0892521422702	0.00655860595022	0.211965584089	0.16351863863	0.141444605668	-0.00879252790502	0.146261112502	0.00424531994041	-0.0031858698618	0.112064603229	-0.043089772613	0.159869486401	-10.0281754284	-38.1720310675	-21.5547237053
10	0.0283316731427	0.021725233484	0.0113386836265	0.0309375700739	0.0159164533644	0.0923429214126	-0.0134610887406	0.0494458492057	-0.0430658380822	-0.219671430403	0.0729750994697	-0.251072355747	-0.198474573453	0.123668969791	0.00780114676738	0.184412617561	-0.024006286703	0.0267621457338	0.117329882621	-0.0242682662144	0.128724176595	0.192165118847	-28.6352353869	-26.7636178709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 114 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 115 through 139 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 140 through 198 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 199 through 272 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 273 through 316 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 317 through 350 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 5 through 11 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 12 through 23 )

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