PDB-2r2p: Kinase domain of human ephrin type-A receptor 5 (EphA5)

ID or keywords:

Entry

Database: PDB / ID: 2r2p

Title

Kinase domain of human ephrin type-A receptor 5 (EphA5)

Components

Ephrin type-A receptor 5

Keywords

TRANSFERASE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / RECEPTOR / PHOSPHORYLATION / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE / Alternative splicing / Glycoprotein / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

positive regulation of CREB transcription factor activity / ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of insulin secretion involved in cellular response to glucose stimulus / transmembrane-ephrin receptor activity / EPH-Ephrin signaling / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / neuron development ...
Similarity search - Function

Ephrin type-A receptor 5, ligand binding domain / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Walker, J.R. / Cuerrier, D. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: Kinase Domain of Human Ephrin Type-A Receptor 5 (EphA5).
Authors: Walker, J.R. / Cuerrier, D. / Butler-Cole, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.

History

Deposition	Aug 27, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 30, 2023	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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r2p.cif.gz	129.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2r2p.ent.gz	101.7 KB	Display	PDB format
PDBx/mmJSON format	2r2p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2r2p_validation.pdf.gz	445.5 KB	Display	wwPDB validaton report
Full document	2r2p_full_validation.pdf.gz	447.3 KB	Display
Data in XML	2r2p_validation.xml.gz	12.9 KB	Display
Data in CIF	2r2p_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/2r2p ftp://data.pdbj.org/pub/pdb/validation_reports/r2/2r2p	HTTPS FTP

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Related structure data

Related structure data	2gsfS S: Starting model for refinement
Similar structure data	1fvr-1 6gqq-d 2wqb-d 6gqp-d 5wdy-1 3ceg-2 5w5q-2 5we8-2 1mdo-d 4bbm-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	#43 - Jul 2003 Src Tyrosine Kinase similarity (3) #60 - Dec 2004 Ubiquitin similarity (3) #185 - May 2015 Titin similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #245 - May 2020 Spliceosomes similarity (1) #88 - Apr 2007 Clathrin similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Ephrin type-A receptor 5

hetero molecules

34 kDa, 1 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)	80.085, 80.085, 169.237
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Ephrin type-A receptor 5 / Tyrosine-protein kinase receptor EHK-1 / EPH homology kinase 1 / Receptor protein-tyrosine kinase HEK7 Mass: 33560.508 Da / Num. of mol.: 1 / Fragment: Kinase domain: Residues 653-939 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA5, EHK1, HEK7 / Plasmid: pNIC-CH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P54756, receptor protein-tyrosine kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.33 Å³/Da / Density % sol: 47.3 %
Crystal grow	Temperature: 298 K / pH: 7.5 Details: 2M Ammonium sulfate, 2% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97918
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2007 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL AND K-B PAIR OF BIOMORPH MIRRORS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.4→44 Å / Num. obs: 13160 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / R_sym value: 0.126 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / R_sym value: 0.87 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSF

2gsf

Resolution: 2.4→43.77 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.881 / SU B: 17.918 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28338	646	4.9 %	RANDOM
R_work	0.19905	-	-	-
obs	0.20291	12435	98.87 %	-
all	-	12435	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0.03 Å²	0 Å²
2-	-	0.07 Å²	0 Å²
3-	-	-	-0.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→43.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2225	0	21	67	2313

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	2292
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.323	1.959	3109
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.991	5	282
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.612	23.627	102
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.431	15	383
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.511	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	340
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1727
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	1030
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	1553
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	87
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	0.174	0.2	62
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.2	12
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	0.459	1.5	1450
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.757	2	2274
X-RAY DIFFRACTION	r_scbond_it	1.377	3	966
X-RAY DIFFRACTION	r_scangle_it	2.131	4.5	835
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	55	-
R_work	0.248	883	-
obs	-	-	99.79 %

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	13.134	-4.9383	-3.3656	10.4149	1.3386	7.8476	0.4001	1.3299	0.1906	-0.5848	-0.5219	0.6881	-0.5108	-0.8263	0.1218	0.2213	0.0027	-0.1066	0.2272	-0.0038	0.1963	-8.9149	51.9933	-2.9952
2	6.8017	4.307	0.1103	12.6798	8.164	21.3022	-0.2618	0.074	0.1953	-0.461	-0.2049	-0.4984	-0.8154	0.3934	0.4666	0.172	-0.021	0.0258	0.0377	0.0273	0.1641	-0.1164	52.1439	0.9272
3	38.5694	-2.5805	22.2048	7.5413	2.0958	25.3101	-0.6436	2.1721	0.5256	-1.1563	0.5043	0.279	-1.0745	0.5044	0.1393	0.2733	-0.0547	0.0282	0.2392	0.0861	0.0395	-7.1889	50.0991	-4.8551
4	5.1029	2.8677	-2.5264	13.2363	-12.4456	30.4264	-0.944	1.3378	0.1114	-1.2925	1.4845	1.9209	0.2475	-1.7728	-0.5405	0.2813	-0.1951	-0.1451	0.5893	0.1419	0.6008	-20.3996	49.4055	-4.0447
5	2.6753	-1.4648	-0.7366	5.7058	-0.8582	2.4142	0.1782	0.2645	0.2607	-0.2258	-0.1734	-0.0327	-0.3065	-0.2217	-0.0048	0.0573	-0.0618	-0.0086	0.1574	-0.0134	0.0686	-8.5363	43.4149	1.6235
6	6.3288	-3.3367	1.3124	6.2565	1.1904	2.2222	0.276	-0.1819	-0.2606	-0.0346	-0.0271	-0.1085	-0.2307	0.395	-0.2489	-0.0026	-0.0415	0.0086	0.036	-0.019	0.0198	-5.997	27.0481	8.2241
7	2.4842	1.4709	-2.0573	5.1564	5.615	12.5993	-0.0282	-0.8559	1.1696	0.2163	0.4896	0.1728	-0.3638	0.314	-0.4614	0.0202	0.0347	0.0091	0.0148	-0.0202	0.1073	-20.5417	34.9219	6.0715
8	14.251	-3.2594	6.8799	6.0965	-1.51	16.9298	0.2944	0.1232	0.5651	0.0961	-0.2269	-0.0258	0.3634	0.613	-0.0674	-0.0163	-0.0812	0.0623	0.0505	-0.0444	0.0451	-4.8671	33.3716	3.0194
9	49.339	-2.1758	2.1676	4.3132	-1.4623	0.5382	0.6483	0.8777	2.4487	-0.7284	0.1943	0.7059	-0.0119	-0.0845	-0.8427	0.0774	-0.0036	-0.051	0.2009	0.0178	0.2463	-18.662	38.3847	2.8034
10	9.7379	-8.8485	6.3683	19.3559	-2.7086	5.0019	0.2681	0.3252	-0.0583	-0.2554	-0.2191	0.7755	-1.8912	-2.8274	-0.049	0.2809	-0.1026	-0.0209	0.5661	0.0345	0.5251	-31.3398	34.7258	3.7951
11	41.7672	-3.7048	-19.6153	0.3336	1.7836	9.5932	-0.6043	0.7502	0.2194	-0.4326	0.434	0.0969	0.2227	-0.5289	0.1703	0.0744	-0.027	-0.0205	0.0031	0.0721	0.0921	-27.2954	24.6056	-0.9046
12	6.3823	0.6681	-0.4864	2.8109	-0.2528	2.4926	0.0347	0.0191	-0.1157	0.1433	0.0675	0.0591	-0.0962	0.0064	-0.1022	0.013	-0.0253	-0.0114	-0.0009	-0.016	-0.0389	-18.2265	24.3031	4.7096
13	0.9232	0.3496	0.7981	3.4701	2.8033	6.7671	0.0202	0.599	-0.2662	-0.4198	-0.1172	0.157	0.1472	-0.7236	0.0971	0.0371	0.0191	-0.0373	0.0938	-0.0578	0.0885	-19.98	16.1601	-5.1138
14	5.6273	1.0154	5.2113	10.966	-0.8517	5.124	0.0191	0.0791	-0.5453	0.0976	0.1555	-0.6249	0.0291	0.6518	-0.1746	0.0394	-0.0001	-0.0343	0.0695	-0.0438	0.1107	-11.1728	13.539	6.9804
15	27.9975	-6.3268	-5.5153	10.8032	4.4957	3.6949	-0.0502	-0.4947	-0.9033	-0.0329	-0.0673	1.0521	0.1713	-0.4369	0.1175	0.0043	0.002	-0.0392	0.0584	0.0444	0.07	-25.3681	19.0049	9.6745
16	19.0599	-1.3537	6.8086	0.2934	-0.1831	2.8898	0.2585	-0.5529	-0.6912	0.1763	0.1081	-0.1247	0.1642	0.0943	-0.3666	0.1391	-0.0507	-0.0659	0.1219	0.0247	0.0975	-6.9468	20.7252	17.1504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	662 - 687	11 - 36
2	X-RAY DIFFRACTION	2	A	A	688 - 700	37 - 49
3	X-RAY DIFFRACTION	3	A	A	701 - 712	50 - 61
4	X-RAY DIFFRACTION	4	A	A	713 - 729	62 - 78
5	X-RAY DIFFRACTION	5	A	A	730 - 766	79 - 115
6	X-RAY DIFFRACTION	6	A	A	767 - 792	116 - 141
7	X-RAY DIFFRACTION	7	A	A	793 - 803	142 - 152
8	X-RAY DIFFRACTION	8	A	A	804 - 814	153 - 163
9	X-RAY DIFFRACTION	9	A	A	815 - 824	164 - 173
10	X-RAY DIFFRACTION	10	A	A	825 - 841	174 - 190
11	X-RAY DIFFRACTION	11	A	A	842 - 853	191 - 202
12	X-RAY DIFFRACTION	12	A	A	854 - 873	203 - 222
13	X-RAY DIFFRACTION	13	A	A	874 - 896	223 - 245
14	X-RAY DIFFRACTION	14	A	A	897 - 912	246 - 261
15	X-RAY DIFFRACTION	15	A	A	913 - 920	262 - 269
16	X-RAY DIFFRACTION	16	A	A	921 - 946	270 - 295

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