PDB-4x21: The MAP kinase JNK3 as target for halogen bonding

ID or keywords:

Entry

Database: PDB / ID: 4x21

Title

The MAP kinase JNK3 as target for halogen bonding

Components

Mitogen-activated protein kinase 10

Keywords

TRANSFERASE / MAPK / halogen bond complex

Function / homology

Function and homology information

JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / response to light stimulus / mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation / regulation of circadian rhythm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Lange, A. / Buettner, F.M. / Guenther, M.B. / Zimmermann, M.O. / Hennig, S. / Laufer, S.A. / Stehle, T. / Boeckler, F.

Citation

Journal: J.Am.Chem.Soc. / Year: 2015
Title: Targeting the Gatekeeper MET146 of C-Jun N-Terminal Kinase 3 Induces a Bivalent Halogen/Chalcogen Bond.
Authors: Lange, A. / Gunther, M. / Buttner, F.M. / Zimmermann, M.O. / Heidrich, J. / Hennig, S. / Zahn, S. / Schall, C. / Sievers-Engler, A. / Ansideri, F. / Koch, P. / Laemmerhofer, M. / Stehle, T. ...

History

Deposition	Nov 25, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 25, 2015	Group: Database references
Revision 1.2	Dec 2, 2015	Group: Database references
Revision 2.0	Jun 3, 2020	Group: Atomic model / Data collection / Derived calculations Category: atom_site / pdbx_nonpoly_scheme / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1	Jan 10, 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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PDBx/mmCIF format	4x21.cif.gz	280.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4x21.ent.gz	225.9 KB	Display	PDB format
PDBx/mmJSON format	4x21.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4x21_validation.pdf.gz	992.9 KB	Display	wwPDB validaton report
Full document	4x21_full_validation.pdf.gz	1010.6 KB	Display
Data in XML	4x21_validation.xml.gz	28.5 KB	Display
Data in CIF	4x21_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/4x21 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x21	HTTPS FTP

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Related structure data

Related structure data	2p33S S: Starting model for refinement
Similar structure data	4h3b-1 2ok1-d 3pze-d 7ksi-d 3cgf-d 3v6r-1 6emh-1 6emh-2 3da6-d 2exc-d 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) #122 - Feb 2010 Enhanceosome similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Mitogen-activated protein kinase 10

B: Mitogen-activated protein kinase 10

hetero molecules

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

1

A: Mitogen-activated protein kinase 10

hetero molecules

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

2

B: Mitogen-activated protein kinase 10

hetero molecules

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

Unit cell

Length a, b, c (Å)	155.940, 109.840, 43.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Mitogen-activated protein kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated ...MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 Mass: 42260.855 Da / Num. of mol.: 2 / Fragment: UNP residues 39-402 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical	ChemComp-3WH / N-ethyl-4-{[4-(1H-indol-3-yl)-5-iodopyrimidin-2-yl]amino}piperidine-1-carboxamide Mass: 490.341 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂₀H₂₃IN₆O
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.08 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: HEPES, sodium chloride, magnesium chloride, beta-mercaptoethanol ethylene glycole, zwittergent 3-14, AMP-PCP Bis-Tris, sodium chloride, PEG 3350, glycerole PH range: 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918409 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. all: 56051 / Num. obs: 56051 / % possible obs: 100 % / Redundancy: 13.2 % / B_iso Wilson estimate: 33.5 Å² / R_merge(I) obs: 0.152 / Net I/σ(I): 14.35
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 13.4 % / R_merge(I) obs: 1.226 / Mean I/σ(I) obs: 2.42 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2P33

2p33

Resolution: 1.95→46.984 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2235	2803	5 %	Random selection
R_work	0.1998	-	-	-
obs	0.201	56049	99.98 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.5 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→46.984 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5195	0	58	342	5595

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	5379
X-RAY DIFFRACTION	f_angle_d	1.241	7321
X-RAY DIFFRACTION	f_dihedral_angle_d	15.615	1937
X-RAY DIFFRACTION	f_chiral_restr	0.078	830
X-RAY DIFFRACTION	f_plane_restr	0.006	926

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 (%)
1.9499-1.9836	0.3098	138	0.2766	2622	X-RAY DIFFRACTION	100
1.9836-2.0196	0.29	137	0.2573	2611	X-RAY DIFFRACTION	100
2.0196-2.0585	0.2733	138	0.247	2609	X-RAY DIFFRACTION	100
2.0585-2.1005	0.2589	140	0.2421	2658	X-RAY DIFFRACTION	100
2.1005-2.1462	0.2702	136	0.2264	2591	X-RAY DIFFRACTION	100
2.1462-2.1961	0.2577	141	0.2116	2678	X-RAY DIFFRACTION	100
2.1961-2.251	0.228	136	0.217	2584	X-RAY DIFFRACTION	100
2.251-2.3119	0.2686	140	0.2166	2659	X-RAY DIFFRACTION	100
2.3119-2.3799	0.2558	137	0.2117	2613	X-RAY DIFFRACTION	100
2.3799-2.4567	0.2304	140	0.2046	2647	X-RAY DIFFRACTION	100
2.4567-2.5445	0.2597	138	0.2055	2626	X-RAY DIFFRACTION	100
2.5445-2.6464	0.2339	139	0.204	2650	X-RAY DIFFRACTION	100
2.6464-2.7668	0.2392	141	0.2024	2665	X-RAY DIFFRACTION	100
2.7668-2.9126	0.2278	140	0.2062	2662	X-RAY DIFFRACTION	100
2.9126-3.0951	0.2369	140	0.2098	2658	X-RAY DIFFRACTION	100
3.0951-3.334	0.2383	140	0.1961	2674	X-RAY DIFFRACTION	100
3.334-3.6694	0.1926	143	0.1845	2710	X-RAY DIFFRACTION	100
3.6694-4.2001	0.1941	141	0.1696	2686	X-RAY DIFFRACTION	100
4.2001-5.2905	0.1581	145	0.1623	2746	X-RAY DIFFRACTION	100
5.2905-46.9981	0.2307	153	0.2105	2897	X-RAY DIFFRACTION	100

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	1.9448	1.0814	0.6047	3.3749	-0.5321	3.1692	-0.0697	-0.0468	0.1464	0.2494	-0.0738	-0.108	-0.0481	-0.1666	0.1384	0.3482	0.0198	0.0367	0.2788	-0.0205	0.1927	12.839	42.7463	80.9679
2	0.5586	0.3851	-1.1374	1.0348	-0.8187	2.2833	-0.164	-0.0685	0.1552	-0.0973	-0.0242	0.0079	0.0915	0.0123	0.1309	0.325	0.0146	-0.0176	0.3895	-0.0237	0.2945	17.4427	45.6987	68.7377
3	0.6863	0.1192	-0.27	1.4618	1.1166	1.7927	0.046	-0.064	0.0198	0.1318	-0.0665	0.0053	-0.0741	-0.0606	0.025	0.1767	-0.0083	-0.0058	0.1811	-0.0078	0.1504	14.4285	34.2079	63.3119
4	2.388	-0.5686	-0.1066	1.4664	0.3439	0.8602	0.0214	-0.1063	0.2742	0.1788	0.0452	-0.1642	-0.1417	0.146	-0.0855	0.2301	-0.0361	-0.0032	0.1962	-0.0333	0.1989	27.4436	28.571	55.4883
5	2.546	0.3826	-0.3178	2.4927	0.7619	1.9006	0.1952	-0.288	-0.2153	0.3168	0.0785	-0.6253	0.0862	0.4372	-0.2241	0.2276	-0.0223	-0.0523	0.2632	-0.0259	0.3141	35.8218	20.3333	58.1723
6	1.5632	0.4685	0.0026	2.005	0.0539	1.545	0.0042	0.0357	-0.1693	-0.1865	0.0618	-0.2953	-0.0231	0.15	-0.0473	0.1782	-0.003	0.0257	0.1722	-0.0461	0.146	26.7743	18.1952	48.1095
7	1.6152	1.5293	1.5833	2.1636	1.7475	2.2517	-0.2872	0.3966	0.2636	-0.3766	0.2647	0.1623	-0.4614	0.3716	-0.0179	0.3292	-0.0073	0.0679	0.3242	0.0453	0.325	16.5555	48.4736	58.0419
8	2.2689	-0.4453	1.3257	0.3501	-0.6533	1.3809	0.1026	-0.1573	-0.9878	-0.0955	0.2778	0.3397	0.3784	-0.2307	-0.3079	0.3738	-0.0433	-0.0529	0.4174	0.1098	0.6438	60.2976	26.5931	72.4414
9	1.8922	-0.4164	0.2971	1.4841	-0.71	1.1769	0.1036	-0.1333	-0.4633	0.0078	-0.0472	-0.0731	0.1424	-0.023	-0.0636	0.2025	-0.0328	-0.0088	0.2472	0.0043	0.2886	56.6816	40.5532	65.3938
10	3.1578	-0.0504	-1.2213	1.7828	-0.154	1.3319	0.006	0.3715	-0.0484	-0.1002	-0.0545	-0.0224	0.0118	-0.1124	0.0302	0.1975	-0.0086	-0.015	0.2391	-0.0055	0.1623	57.8893	56.7129	53.3777
11	4.9218	-3.3308	2.5734	1.9676	-1.7786	1.3211	-0.5052	-1.2768	0.0606	0.2072	0.5696	0.0579	0.0099	-0.547	-0.0919	0.3805	0.0689	0.0139	0.6023	0.0326	0.4187	56.9889	41.4776	77.4378

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 46 through 83 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 84 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 205 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 206 through 258 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 259 through 279 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 280 through 362 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 363 through 400 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 47 through 130 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 131 through 241 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 242 through 355 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 356 through 400 )

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