PDB-6hmr: Crystal structure of human Casein Kinase I delta in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 6hmr

Title

Crystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azothiazole-based inhibitor (compound 2)

Components

Casein kinase I isoform delta

Keywords

TRANSFERASE / Kinase / Photoswitchable Inhibitor / Complex

Function / homology

Function and homology information

positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / tau-protein kinase / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.782 Å

Authors

Pichlo, C. / Schehr, M. / Charl, J. / Brunstein, E. / Peifer, C. / Baumann, U.

Citation

Journal: Photochem. Photobiol. Sci. / Year: 2019
Title: 2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach.
Authors: Schehr, M. / Ianes, C. / Weisner, J. / Heintze, L. / Muller, M.P. / Pichlo, C. / Charl, J. / Brunstein, E. / Ewert, J. / Lehr, M. / Baumann, U. / Rauh, D. / Knippschild, U. / Peifer, C. / Herges, R.

History

Deposition	Sep 12, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2019	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	6hmr.cif.gz	357.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6hmr.ent.gz	297.1 KB	Display	PDB format
PDBx/mmJSON format	6hmr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6hmr_validation.pdf.gz	964.6 KB	Display	wwPDB validaton report
Full document	6hmr_full_validation.pdf.gz	970.7 KB	Display
Data in XML	6hmr_validation.xml.gz	27.6 KB	Display
Data in CIF	6hmr_validation.cif.gz	40.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/6hmr ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hmr	HTTPS FTP

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Related structure data

Related structure data	6hmpC 6hwtC 6hwuC 6hwvC 5mqvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hmp-1 2o27-2 5mqv-1 5z6u-2 5okt-3 3uyt-2 5mqv-2 3edw-d 5mqv-4 4kb8-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#60 - Dec 2004 Ubiquitin similarity (1) #53 - May 2004 Serpins similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #86 - Feb 2007 Exosomes similarity (1)

Deposited unit

A: Casein kinase I isoform delta

B: Casein kinase I isoform delta

hetero molecules

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

1

A: Casein kinase I isoform delta

hetero molecules

defined by author
37 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Casein kinase I isoform delta

hetero molecules

defined by author
37 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.880, 74.036, 89.485
Angle α, β, γ (deg.)	90.00, 102.82, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D Mass: 36377.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical	ChemComp-GE5 / 3-(2,5-dimethoxyphenyl)-~{N}-[4-[4-(4-fluorophenyl)-2-[(~{E})-phenyldiazenyl]-1,3-thiazol-5-yl]pyridin-2-yl]propanamide Mass: 567.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₁H₂₆FN₅O₃S
#3: Chemical	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium malonate pH 6.0 20 % Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000031 Å / Relative weight: 1
Reflection	Resolution: 1.782→46.38 Å / Num. obs: 57955 / % possible obs: 97.37 % / Redundancy: 7 % / Net I/σ(I): 11.23
Reflection shell	Resolution: 1.782→1.846 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: 000)	refinement
XDS	20180126	data reduction
XDS	20180126	data scaling
PHASER	(1.12_2829: 000)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5MQV

5mqv

Resolution: 1.782→46.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 23.23

	R_factor	Num. reflection	% reflection
R_free	0.1993	1896	3.27 %
R_work	0.1751	-	-
obs	0.1759	57936	97.3 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.782→46.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4589	0	96	462	5147

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4848
X-RAY DIFFRACTION	f_angle_d	0.849	6532
X-RAY DIFFRACTION	f_dihedral_angle_d	13.47	2846
X-RAY DIFFRACTION	f_chiral_restr	0.05	671
X-RAY DIFFRACTION	f_plane_restr	0.006	836

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 (%)
1.7817-1.8262	0.3313	119	0.3399	3849	X-RAY DIFFRACTION	94
1.8262-1.8756	0.34	148	0.301	3960	X-RAY DIFFRACTION	96
1.8756-1.9308	0.3021	129	0.2883	3904	X-RAY DIFFRACTION	96
1.9308-1.9931	0.2759	137	0.2457	3933	X-RAY DIFFRACTION	96
1.9931-2.0643	0.2627	137	0.22	3991	X-RAY DIFFRACTION	97
2.0643-2.147	0.2135	134	0.1984	3970	X-RAY DIFFRACTION	97
2.147-2.2447	0.2307	125	0.1837	4013	X-RAY DIFFRACTION	97
2.2447-2.3631	0.2389	151	0.1814	3991	X-RAY DIFFRACTION	97
2.3631-2.5111	0.1774	128	0.1682	3996	X-RAY DIFFRACTION	98
2.5111-2.705	0.1916	138	0.1609	4045	X-RAY DIFFRACTION	98
2.705-2.9771	0.1948	138	0.1616	4043	X-RAY DIFFRACTION	98
2.9771-3.4078	0.1751	141	0.1536	4075	X-RAY DIFFRACTION	99
3.4078-4.2931	0.1537	134	0.1379	4087	X-RAY DIFFRACTION	99
4.2931-47.6793	0.1652	137	0.153	4183	X-RAY DIFFRACTION	99

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	7.4509	1.8632	4.1988	2.4277	0.692	4.5889	-0.1291	0.0941	0.2754	-0.1031	0.0887	-0.0313	-0.3369	0.0784	0.0216	0.1879	-0.0161	0.0617	0.2591	0.0135	0.2193	11.4199	5.6167	16.365
2	3.3713	4.535	2.606	7.6345	1.5812	4.8849	-0.0684	0.0561	-0.2209	-0.0359	0.0404	-0.4029	0.287	0.3055	0.0424	0.181	0.0218	0.0453	0.2135	-0.0074	0.2198	8.7671	-6.9014	24.6405
3	3.4015	4.4252	-2.3512	6.8925	-1.2229	7.0822	0.0237	0.5337	-0.5595	0.0347	-0.0686	-0.6174	0.3431	0.3409	0.0846	0.1552	0.0384	0.0449	0.3535	-0.0109	0.3429	14.8444	0.0056	16.3884
4	0.8503	0.9048	0.9846	5.9071	0.6672	5.6588	0.2404	-0.1045	0.4508	-0.1325	0.0041	0.038	-0.3703	0.0577	-0.1666	0.126	-0.007	-0.0034	0.1534	0.0269	0.1099	-10.5209	8.1295	21.0127
5	2.8378	-0.8363	1.1512	1.1641	-0.7311	3.52	0.0371	0.0873	-0.1264	-0.0793	-0.0051	-0.073	0.2311	0.2702	-0.046	0.1405	-0.012	0.0118	0.127	-0.0106	0.1672	-1.1959	-4.54	31.1386
6	1.3295	-0.5071	1.3507	2.3403	-1.7158	4.6644	-0.0121	-0.077	0.052	0.1169	-0.0264	-0.1828	-0.2935	0.2078	0.0689	0.1617	-0.0222	0.0142	0.2026	-0.0129	0.1578	-2.2265	5.1952	40.6294
7	8.0543	1.3292	0.4256	6.4382	-2.3535	7.3543	0.2048	-0.436	0.5886	0.3876	-0.1872	-0.2662	-0.7174	0.4871	0.0293	0.3217	-0.0153	0.0429	0.2555	-0.0649	0.308	-4.4437	17.7722	42.1089
8	2.824	-0.7307	0.3283	1.821	-0.4109	3.4808	0.0403	-0.3136	-0.0346	0.0693	0.0147	0.0832	-0.0965	-0.3077	-0.0696	0.1446	-0.0222	0.0118	0.2902	0.0103	0.1484	-12.7372	0.4624	43.5956
9	2.5879	-0.5041	1.6828	0.3518	0.3063	2.5935	0.1118	-0.0988	-0.3741	-0.0177	-0.0323	0.1105	0.3001	-0.3322	-0.1291	0.1722	-0.0486	-0.0002	0.1982	-0.0013	0.2305	-18.9302	-4.8056	27.5898
10	2.861	0.3807	0.2231	3.3881	2.3317	7.2521	-0.0466	-0.4534	0.1712	0.4221	0.0236	0.3058	-0.3877	-0.4021	0.0429	0.3815	0.0323	0.0645	0.3704	0.001	0.2534	5.9937	-26.5429	-4.4426
11	4.4186	1.5171	0.515	4.3048	-2.787	7.0221	-0.1995	-0.0374	0.1229	0.3501	-0.136	-0.2157	-0.6214	0.7245	0.248	0.2653	-0.0346	0.0027	0.4112	0.0116	0.2623	10.7712	-31.1996	7.7887
12	3.9847	3.8136	-3.222	4.7022	-5.38	8.9418	-0.0281	0.4445	0.2724	0.5011	-0.3094	-0.2988	-0.7699	1.1017	0.2504	0.4685	-0.0627	-0.0349	0.7552	0.0826	0.4194	12.9798	-26.9375	1.5762
13	1.9509	0.608	1.0623	0.9948	0.2514	2.9638	-0.0558	0.0624	-0.0441	-0.0247	0.0582	-0.0795	-0.0083	0.2956	-0.0259	0.1646	0.0346	0.0147	0.2286	0.0077	0.1623	-0.4114	-37.9648	15.4819
14	1.9432	1.0854	0.5704	2.7118	1.0629	4.0817	0.0155	-0.0698	0.2622	-0.0273	-0.0113	0.0349	-0.3024	0.0911	-0.0012	0.1905	0.0309	0.0227	0.2056	0.0019	0.1677	-4.648	-29.6227	25.3665
15	4.2802	2.8819	-0.0054	4.9523	-0.1365	4.8096	0.175	-0.0053	0.3095	0.2038	-0.1658	0.18	-0.4177	-0.4623	0.0215	0.2056	0.1097	0.0305	0.3379	0.0086	0.2322	-17.5445	-30.6782	26.4349
16	4.2957	3.3604	2.4222	4.9891	1.9374	4.441	0.1245	-0.292	0.0132	0.2244	-0.0477	-0.0481	0.1821	0.2147	-0.0563	0.1877	0.0161	0.0125	0.262	0.0106	0.1435	-4.6853	-39.5308	31.7912
17	9.2393	9.2548	8.7604	9.5135	8.7384	8.2687	0.1012	0.1117	-0.3591	0.1304	0.1062	-0.1693	0.3738	0.1123	-0.1383	0.2418	0.0216	0.0046	0.1911	0.0645	0.2103	-8.1001	-50.7914	23.7431
18	4.887	4.6633	-3.9902	8.0429	-4.4555	3.3817	-0.1165	0.4716	-0.3652	-0.3392	0.2751	0.1004	0.2672	-0.6488	-0.2114	0.2629	-0.0033	-0.036	0.2951	-0.0357	0.2502	-13.2981	-49.7427	8.4636

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 167 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 168 through 208 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 209 through 234 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 235 through 265 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 266 through 294 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 32 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 33 through 67 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 83 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 84 through 167 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 168 through 208 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 209 through 246 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 247 through 265 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 266 through 279 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 280 through 293 )

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