PDB-3qfv: MRCK beta in complex with TPCA-1

ID or keywords:

Entry

Database: PDB / ID: 3qfv

Title

MRCK beta in complex with TPCA-1

Components

CDC42BPB protein

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase domain of MRCK beta in complex with TPCA-1 / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

actomyosin / actomyosin structure organization / establishment or maintenance of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / cell leading edge / CDC42 GTPase cycle / cytoskeleton organization /

small GTPase binding / cell-cell junction ...
Similarity search - Function

Serine/threonine-protein kinase MRCK beta / Serine/threonine-protein kinase MRCK beta, catalytic domain / KELK-motif containing domain / KELK-motif containing domain of MRCK Ser/Thr protein kinase /

Myotonic dystrophy protein kinase, coiled coil / DMPK coiled coil domain like / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Heikkila, T.J. / Wheatley, E. / Crighton, D. / Schroder, E. / Boakes, A. / Kaye, S.J. / Mezna, M. / Pang, L. / Rushbrooke, M. / Turnbull, A. / Olson, M.F.

Citation

Journal: Plos One / Year: 2011
Title: Co-crystal structures of inhibitors with MRCK beta , a key regulator of tumor cell invasion.
Authors: Heikkila, T. / Wheatley, E. / Crighton, D. / Schroder, E. / Boakes, A. / Kaye, S.J. / Mezna, M. / Pang, L. / Rushbrooke, M. / Turnbull, A. / Olson, M.F.

History

Deposition	Jan 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qfv.cif.gz	324.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3qfv.ent.gz	267.3 KB	Display	PDB format
PDBx/mmJSON format	3qfv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/3qfv ftp://data.pdbj.org/pub/pdb/validation_reports/qf/3qfv	HTTPS FTP

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Related structure data

Related structure data	3tkuC 3my4 PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4aw2-1 3tku-d 3ndm-1 3tv7-2 4wot-1 4uak-1 5wng-1 5wnf-2 2etr-d 5bml-d 5kks-d 6e9w-1 5u7q-6 3ncz-2 3v8s-1 5wng-2 6p5p-5 3tv7-1 5kkt-d 5wnh-1 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	#195 - Mar 2016 RAF Protein Kinases similarity (6) #196 - Apr 2016 Lead Poisoning similarity (9) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (6) #35 - Nov 2002 Ferritin and Transferrin similarity (3) #183 - Mar 2015 Phototropin similarity (3)

Deposited unit

A: CDC42BPB protein

B: CDC42BPB protein

hetero molecules

96.3 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)	44.810, 123.360, 85.490
Angle α, β, γ (deg.)	90.00, 100.69, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	CDC42BPB protein Mass: 47737.125 Da / Num. of mol.: 2 / Fragment: unp residues 1-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42BPB, MRCK beta / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XZ8, UniProt: Q9Y5S2*PLUS

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Non-polymers , 5 types, 124 molecules

#2: Chemical	ChemComp-NM7 / 2-(carbamoylamino)-5-(4-fluorophenyl)thiophene-3-carboxamide Mass: 279.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₀FN₃O₂S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.43 Å³/Da / Density % sol: 49.42 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.63→44.03 Å / Num. all: 25154 / Num. obs: 25154 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MRCK beta in complex with Fasudil

Resolution: 2.65→39.97 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.878 / SU B: 29.304 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26757	1254	5 %	RANDOM
R_work	0.19215	-	-	-
obs	0.19599	23670	94.27 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 41.844 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.82 Å²	0 Å²	0.73 Å²
2-	-	-1.58 Å²	0 Å²
3-	-	-	3.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→39.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6226	0	53	116	6395

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6420
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.609	1.959	8700
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.17	5	787
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.951	24.242	297
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.355	15	1054
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.438	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	952
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	4900
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.629	1.5	3928
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.227	2	6295
X-RAY DIFFRACTION	r_scbond_it	1.89	3	2492
X-RAY DIFFRACTION	r_scangle_it	3.145	4.5	2405
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	81	-
R_work	0.254	1630	-
obs	-	-	89.3 %

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	1.7196	3.974	-0.3705	7.9798	0.9489	2.678	-0.2899	0.3945	-0.2124	-0.7457	0.2026	-0.4279	0.1944	-0.037	0.0873	0.1764	0.1615	0.0717	0.3298	0.038	0.2337	12.9141	-42.1173	11.4714
2	1.3252	1.3824	0.1093	5.6648	1.9258	0.5913	0.2649	-0.2376	0.004	0.5825	-0.3806	0.3964	0.1028	-0.1851	0.1157	0.1341	-0.0332	0.0562	0.2068	-0.0145	0.1199	-7.4921	-48.0217	26.8955
3	0.7949	0.0315	0.1197	2.1025	0.5657	0.2074	0.0716	0.0155	0.0245	0.0325	-0.1159	0.0972	0.0295	-0.1328	0.0443	0.0678	-0.0371	0.0156	0.1771	-0.0266	0.1072	-3.6313	-68.8671	18.2734
4	0.532	-0.3604	0.5013	1.999	1.3867	1.8086	0.0519	0.0066	0.0807	-0.0807	-0.031	-0.0569	-0.0071	-0.0892	-0.0208	0.1006	-0.0585	0.0128	0.14	0.0124	0.1137	5.9582	-74.9453	15.3225
5	0.7956	-1.809	1.5397	4.7172	-0.3079	2.8224	-0.1102	-0.0897	0.2715	1.1325	0.3055	-0.3447	0.2096	0.214	-0.1952	0.3487	-0.0033	-0.0326	0.1765	-0.0878	0.2291	13.8829	-74.8158	31.2555
6	1.8181	3.1033	0.1698	5.8031	1.5085	0.8018	0.1184	-0.1564	0.1485	0.3248	-0.133	0.1332	0.175	0.0141	0.0146	0.125	-0.0592	-0.0379	0.1382	0.0126	0.174	13.1622	-80.6775	23.6869
7	4.838	2.4477	0.922	9.5794	4.721	8.5469	0.26	-0.7473	-0.7268	1.0638	-0.4188	-0.2325	0.7966	-0.4102	0.1588	0.132	-0.0634	-0.0143	0.1114	0.11	0.0975	9.1177	-91.8403	29.6442
8	3.6746	1.2955	0.9825	4.2785	0.3707	1.4213	0.1386	0.0817	-0.1703	-0.0652	-0.0371	-0.4756	0.2033	0.3275	-0.1016	0.0376	0.0198	-0.0055	0.0928	-0.0349	0.1825	17.1463	-89.0449	14.7666
9	3.4774	-0.6045	-0.1515	6.3325	1.9548	0.6668	0.2177	0.6109	-0.5205	-0.0937	-0.3473	0.6268	0.0492	-0.2138	0.1296	0.0593	-0.0384	-0.0777	0.1516	-0.0111	0.1329	-3.4657	-75.442	10.1256
10	1.3483	0.9119	-0.1542	3.9884	-4.3743	4.4954	-0.1306	0.0512	0.0044	-0.1665	-0.0319	-0.1542	0.0233	0.0762	0.1625	0.1193	0.0088	0.0333	0.1128	-0.0366	0.1215	1.212	-52.1268	15.1959
11	-0.1227	-0.7272	1.6744	4.7752	-3.1602	3.1129	-0.1913	0.2465	0.2388	-0.7293	-0.24	0.3403	-0.0989	0.2173	0.4313	0.2878	0.1382	-0.1612	0.246	0.001	0.4043	-6.1849	-40.2302	11.4167
12	1.5545	2.4169	-0.943	6.715	-2.5573	0.7781	0.3843	-0.3526	0.1304	0.6476	-0.6033	-0.6264	-0.1443	0.2475	0.219	0.1849	-0.0767	-0.0553	0.1886	0.0397	0.2593	14.1469	-34.6745	26.7612
13	2.2642	0.5977	-0.3205	2.2099	-0.5362	0.979	-0.0174	-0.0439	-0.0456	0.0447	-0.1768	-0.19	0.2083	0.0752	0.1942	0.0804	-0.0114	0.0069	0.1095	0.0537	0.0998	10.4353	-19.6424	20.9753
14	2.1732	-1.4087	0.1337	4.3371	-1.5281	0.5089	0.036	0.0826	0.1541	0.0649	-0.1301	-0.2595	-0.0334	0.0847	0.0941	0.0932	-0.0241	-0.0245	0.1391	0.0273	0.0679	7.0682	-7.3438	14.8639
15	2.0137	-0.4682	-0.8719	2.2048	-0.2274	1.2475	0.0999	-0.1326	-0.073	0.2398	0.0025	0.1209	0.0288	0.0678	-0.1024	0.0933	-0.0527	-0.0164	0.1419	0.013	0.0336	-2.4069	-8.4596	24.0273
16	5.0695	4.4963	-1.4414	7.5964	-1.8444	-0.0583	0.1206	-0.2167	0.0213	0.2766	-0.0753	0.1267	-0.0979	0.0374	-0.0452	0.153	-0.0546	-0.0212	0.0835	-0.011	0.1369	-4.7285	1.33	21.6929
17	2.0953	-0.3833	-2.1117	10.3605	-6.9408	5.6887	0.2865	-0.4605	0.6582	1.0824	-0.0868	-0.2082	-0.9259	0.439	-0.1997	0.3033	-0.198	0.0254	0.1802	-0.113	0.1427	-3.0751	10.8913	29.9176
18	4.364	1.6567	0.8847	8.0275	-2.1989	2.2591	0.2714	-0.0483	-0.0416	-0.1462	-0.1077	0.6072	-0.3036	-0.3485	-0.1637	0.1604	0.0791	-0.0097	0.1541	-0.0085	0.1965	-11.7624	4.8783	14.7572
19	3.7237	-1.1512	-1.5564	6.6488	-1.292	0.4475	0.9432	0.9212	0.3795	-0.7142	-0.9109	-0.6011	0.0846	-0.0253	-0.0323	0.3297	0.0539	0.1277	0.2974	0.0052	0.1007	8.5772	-6.0104	8.6156
20	0.6453	1.7408	-0.3313	4.6813	3.3533	8.1289	-0.0063	0.0494	-0.0169	-0.1502	-0.0857	-0.0308	0.0061	-0.1003	0.092	0.0608	0.0674	-0.0284	0.1221	0.0378	0.2167	5.5265	-30.5807	18.0981

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 28
2	X-RAY DIFFRACTION	2	A	29 - 90
3	X-RAY DIFFRACTION	3	A	91 - 178
4	X-RAY DIFFRACTION	4	A	179 - 223
5	X-RAY DIFFRACTION	5	A	224 - 254
6	X-RAY DIFFRACTION	6	A	255 - 273
7	X-RAY DIFFRACTION	7	A	274 - 303
8	X-RAY DIFFRACTION	8	A	304 - 345
9	X-RAY DIFFRACTION	9	A	346 - 396
10	X-RAY DIFFRACTION	10	A	397 - 415
11	X-RAY DIFFRACTION	11	B	2 - 28
12	X-RAY DIFFRACTION	12	B	29 - 90
13	X-RAY DIFFRACTION	13	B	91 - 134
14	X-RAY DIFFRACTION	14	B	135 - 192
15	X-RAY DIFFRACTION	15	B	193 - 256
16	X-RAY DIFFRACTION	16	B	257 - 277
17	X-RAY DIFFRACTION	17	B	278 - 307
18	X-RAY DIFFRACTION	18	B	308 - 343
19	X-RAY DIFFRACTION	19	B	344 - 393
20	X-RAY DIFFRACTION	20	B	394 - 415

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