PDB-8jbn: Vascular endothelial protein tyrosine phosphatase in complex with...

ID or keywords:

Entry

Database: PDB / ID: 8jbn

Title

Vascular endothelial protein tyrosine phosphatase in complex with Cpd-1

Components

Receptor-type tyrosine-protein phosphatase beta

Keywords

HYDROLASE / Protein tyrosine phosphatase / FBDD / Inhibitor

Function / homology

Function and homology information

glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / osteoblast differentiation / angiogenesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Orita, T. / Furuzono, T. / Doi, S. / Adachi, T.

Funding support

1items

Citation

Journal: Biochemistry / Year: 2023
Title: Fragment-Based Discovery of Novel VE-PTP Inhibitors Using Orthogonal Biophysical Techniques.
Authors: Asano, W. / Yamanaka, K. / Ohara, Y. / Uhara, T. / Doi, S. / Orita, T. / Iwanaga, T. / Adachi, T. / Fujioka, S. / Akaki, T. / Ikegashira, K. / Hantani, Y.

History

Deposition	May 9, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jbn.cif.gz	388.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8jbn.ent.gz	291.1 KB	Display	PDB format
PDBx/mmJSON format	8jbn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8jbn_validation.pdf.gz	714.3 KB	Display	wwPDB validaton report
Full document	8jbn_full_validation.pdf.gz	715.4 KB	Display
Data in XML	8jbn_validation.xml.gz	25.2 KB	Display
Data in CIF	8jbn_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/8jbn ftp://data.pdbj.org/pub/pdb/validation_reports/jb/8jbn	HTTPS FTP

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Related structure data

Related structure data	8jbyC C: citing same article (ref.)
Similar structure data	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	#126 - Jun 2010 Epidermal Growth Factor similarity (12) #145 - Jan 2012 Messenger RNA Capping similarity (5) #225 - Sep 2018 Phytase similarity (5) #185 - May 2015 Titin similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Receptor-type tyrosine-protein phosphatase beta

B: Receptor-type tyrosine-protein phosphatase beta

hetero molecules

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

1

A: Receptor-type tyrosine-protein phosphatase beta

hetero molecules

defined by author
Evidence: gel filtration
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Receptor-type tyrosine-protein phosphatase beta

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.467, 123.467, 178.909
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

Components on special symmetry positions

ID	Model	Components
1	1	A-6237- HOH

#1: Protein	Receptor-type tyrosine-protein phosphatase beta / Protein-tyrosine phosphatase beta / R-PTP-beta / Vascular endothelial protein tyrosine phosphatase / VE-PTP Mass: 34056.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB, PTPB / Production host: Escherichia coli (E. coli) / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-U7C / 5-(1~{H}-indol-3-yl)-1,2-oxazole-3-carboxylic acid Mass: 228.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₈N₂O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H₂O
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: 3.05 Å³/Da / Density % sol: 59.69 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 100mM HEPES, 9.5%(v/v) PEG 6000, 8.8%(v/v) ethylene glycol, soaking the crystal with 6.25 mM Cpd-1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.99→91.78 Å / Num. obs: 104165 / % possible obs: 99.6 % / Redundancy: 19.9 % / B_iso Wilson estimate: 36.4 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.171 / R_pim(I) all: 0.039 / R_rim(I) all: 0.176 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.99→2.04 Å / Redundancy: 19.5 % / R_merge(I) obs: 3.232 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3785 / CC_1/2: 0.71 / R_pim(I) all: 0.736 / R_rim(I) all: 3.316 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
DIALS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→53.46 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.7424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1978	5198	4.99 %
R_work	0.1693	98967	-
obs	0.1707	104165	99.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 47.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.99→53.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4533	0	44	371	4948

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0033	4739
X-RAY DIFFRACTION	f_angle_d	0.5801	6439
X-RAY DIFFRACTION	f_chiral_restr	0.0444	685
X-RAY DIFFRACTION	f_plane_restr	0.0049	843
X-RAY DIFFRACTION	f_dihedral_angle_d	11.124	1772

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 (%)
1.99-2.01	0.2666	202	0.2673	3207	X-RAY DIFFRACTION	98.67
2.01-2.04	0.2747	146	0.2601	3316	X-RAY DIFFRACTION	99.45
2.04-2.06	0.2712	183	0.2392	3292	X-RAY DIFFRACTION	99.46
2.06-2.09	0.2872	193	0.2334	3264	X-RAY DIFFRACTION	98.57
2.09-2.11	0.2831	159	0.2264	3280	X-RAY DIFFRACTION	99.19
2.11-2.14	0.2675	172	0.2356	3290	X-RAY DIFFRACTION	99.63
2.14-2.17	0.2459	180	0.2191	3307	X-RAY DIFFRACTION	98.92
2.17-2.21	0.2827	179	0.209	3284	X-RAY DIFFRACTION	99.57
2.21-2.24	0.2485	223	0.1896	3271	X-RAY DIFFRACTION	99.54
2.24-2.28	0.1969	197	0.1851	3226	X-RAY DIFFRACTION	99.74
2.28-2.32	0.2018	186	0.1792	3305	X-RAY DIFFRACTION	99.74
2.32-2.36	0.2157	157	0.1766	3316	X-RAY DIFFRACTION	99.66
2.36-2.4	0.189	187	0.1809	3267	X-RAY DIFFRACTION	99.22
2.4-2.45	0.2423	173	0.1774	3289	X-RAY DIFFRACTION	99.31
2.45-2.51	0.2131	193	0.1627	3296	X-RAY DIFFRACTION	99.89
2.51-2.57	0.2083	141	0.1696	3350	X-RAY DIFFRACTION	99.66
2.57-2.63	0.207	163	0.1818	3324	X-RAY DIFFRACTION	99.89
2.63-2.7	0.2593	155	0.1696	3324	X-RAY DIFFRACTION	99.91
2.7-2.78	0.1865	171	0.1769	3302	X-RAY DIFFRACTION	99.86
2.78-2.87	0.2172	189	0.1789	3325	X-RAY DIFFRACTION	99.94
2.87-2.97	0.1882	173	0.1669	3285	X-RAY DIFFRACTION	99.91
2.97-3.09	0.1858	188	0.1658	3322	X-RAY DIFFRACTION	99.97
3.09-3.23	0.2009	145	0.1592	3289	X-RAY DIFFRACTION	99.08
3.23-3.4	0.1993	148	0.1722	3340	X-RAY DIFFRACTION	99.97
3.4-3.62	0.1808	149	0.158	3345	X-RAY DIFFRACTION	100
3.62-3.89	0.1684	164	0.1462	3326	X-RAY DIFFRACTION	100
3.9-4.29	0.1436	154	0.1325	3348	X-RAY DIFFRACTION	100
4.29-4.91	0.1382	191	0.129	3245	X-RAY DIFFRACTION	98.82
4.91-6.18	0.2168	140	0.1606	3353	X-RAY DIFFRACTION	100
6.18-53.46	0.2213	197	0.2046	3279	X-RAY DIFFRACTION	99.46

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	0.589773367538	0.203777443216	-0.423859450431	0.587719286914	-0.607748370201	0.713321468176	0.0424234446726	-0.206391028863	0.434812571667	0.385192148378	0.0568994040768	-0.122674189293	-0.625713586043	0.410236613885	-1.1624191864E-6	0.490024963701	-0.0498646107601	-0.0111738908716	0.520298517091	-0.0550940719981	0.489840229977	40.6955405978	84.5438565304	-6.84717376229
2	3.25135284456	0.267605412469	-1.09574675771	1.51667362172	0.738903708253	2.51051562842	0.0183084929151	-0.366344580066	-0.382218442069	0.266902957346	-0.12824698941	-0.228749034018	0.304827108441	0.0535347869771	-0.00705863627476	0.245578635599	-0.00189248175239	-0.0503072143957	0.412027301798	0.00910272288181	0.308071054688	33.5533642685	56.2125648072	5.29641371462
3	1.73646079716	0.134200783037	-0.953962204986	2.25297525512	0.41618141343	0.627524908597	0.0664010626364	-0.165816714622	-0.184996264595	-0.0919600986181	-0.15388756889	0.339953838934	0.261340590617	-0.181163968075	-3.47810964606E-7	0.318877723438	-0.0812043281815	0.0190000078691	0.491938531331	-0.0640261663733	0.311087670155	21.4032018078	61.6413293437	9.02181569123
4	2.57131222421	1.17908283499	-0.820523375336	2.22424574363	-0.313377436794	2.78074000469	0.224828678193	-0.383376683722	0.234100481837	0.302131790944	-0.237083205369	0.31455711584	-0.171023362206	-0.17759732872	-0.00281961782774	0.293289614805	-0.0203932984584	0.0304974008414	0.47676071302	-0.133382173953	0.311895954544	24.6433194652	72.3752648981	9.16557068922
5	0.250214311679	0.185933641595	0.104639691858	0.638425379589	0.585463447057	0.608366994909	-0.0227425888178	-0.619101541996	-0.564883326955	0.861480593266	0.002768370743	-0.528412556455	0.202549796855	0.787550695369	-0.00150213461141	0.700475709365	0.217051431351	-0.0650998394507	0.738725471399	0.0969157167386	0.854338891011	22.9980669939	25.4338209215	6.74162151378
6	0.55519660932	0.260412141164	-0.0544157357585	0.372290920067	0.273752735519	0.361845463012	0.00248943369249	-0.182964846359	-0.140290940142	-0.280951703771	0.245809690244	-0.249394508158	-0.0431490553529	0.313648874396	3.61905248258E-5	0.254476423585	-0.0289382145589	0.00460790221212	0.462789357709	-0.0523072483476	0.35444707396	19.8765911028	45.400484036	-3.18884045069
7	1.07517177358	-0.174695749832	-0.0553720876378	0.52838667801	0.496454756166	0.797638600621	0.0390936120481	0.510186594174	0.228627019086	-0.564439929906	-0.0983245572657	0.0357159260841	-0.171491353747	0.301048121165	-0.000111323527619	0.358077039767	-0.028142480502	-0.0283420407277	0.496782152663	0.00408018061477	0.429580106375	13.191839133	43.6375051449	-12.0423374017
8	2.71654152387	0.227645725908	-0.397226197349	2.01778447196	-0.451723966739	2.17524892273	0.0524526807021	-0.163497076807	-0.111022791673	0.11105201036	0.0210630416283	-0.0579895186304	0.0929812745087	0.0188790491665	4.31056290556E-7	0.211817205355	-0.00884353240172	-0.0176844902338	0.337987753313	0.0239509064068	0.292944689312	5.05427123278	39.8117674542	-1.74499489954
9	2.19366381719	-0.0912317674304	-0.421011982306	1.26012468524	0.911159796072	1.06897973082	0.0824585885148	-0.39019060136	0.272598617591	0.174328151125	-0.103500373897	0.213708252658	-0.244568536875	-0.166497435628	-4.92889561125E-7	0.254682801549	-0.0224982384478	0.0320637105665	0.44163153125	0.00789883422609	0.403179634137	-6.01405052756	46.4476536136	1.22875531874
10	2.61959158851	-0.350462264692	-0.342982655987	2.0249164118	1.25276476429	1.64844933285	-0.00877380544033	-0.266619712137	-0.263424648886	0.298885116109	-0.0146694328338	0.138714780894	0.424094977018	-0.130175508683	-6.79890656956E-7	0.332323911657	-0.097761243671	0.050798764602	0.442354272096	0.0847744046683	0.433560078231	-2.3230187402	34.6943940481	3.69151819536
11	0.829956953255	-0.395304700837	-0.591020194917	0.763944762637	-0.453460332596	1.35330297494	-0.0217709523272	-0.160521929304	-0.478839223138	-0.0587992452597	0.0340795971015	0.103857463677	0.711042629689	-0.0299261991723	8.77671901837E-7	0.461061685052	-0.0547798937936	-0.0328008940772	0.372251950819	0.0758812173569	0.448575189891	4.1246047835	28.3805824383	1.4471190817
12	0.524619459927	-0.0997936987155	-0.122476968753	0.0376088115444	-0.0834965544308	0.671964835616	-0.223421290014	-0.330648623165	-0.771107038379	0.452976277437	0.166861308538	-0.0828072117638	0.721409294237	0.298586382188	0.0195617872311	0.6235869199	0.101958483543	0.0330972876977	0.439914688416	0.111236829102	0.701468450427	14.9209207504	24.6300120459	2.77114616779
13	0.352716413235	-0.0818561903196	-0.250877955408	0.234371770836	0.0405313172278	0.180324875823	0.156272489229	-0.474750927577	-0.350261100228	0.743307076248	-0.109331871758	0.00792820662707	1.00627548497	0.0788125681945	0.0132678343034	0.988882994293	-0.0386795647417	-0.0804747259492	0.648710810996	0.269158632149	0.649456234368	7.35611044939	19.4872273606	14.2732909551

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1687 through 1710 )	A	A	1687 - 1710	1 - 24
2	2	chain 'A' and (resid 1711 through 1782 )	A	A	1711 - 1782	25 - 96
3	3	chain 'A' and (resid 1783 through 1810 )	A	A	1783 - 1810	97 - 124
4	4	chain 'A' and (resid 1811 through 1968 )	A	A	1811 - 1968	125 - 282
5	5	chain 'B' and (resid 1696 through 1720 )	B	E	1696 - 1720	1 - 25
6	6	chain 'B' and (resid 1721 through 1740 )	B	E	1721 - 1740	26 - 45
7	7	chain 'B' and (resid 1741 through 1763 )	B	E	1741 - 1763	46 - 68
8	8	chain 'B' and (resid 1764 through 1810 )	B	E	1764 - 1810	69 - 115
9	9	chain 'B' and (resid 1811 through 1850 )	B	E	1811 - 1850	116 - 155
10	10	chain 'B' and (resid 1851 through 1892 )	B	E	1851 - 1892	156 - 197
11	11	chain 'B' and (resid 1893 through 1926 )	B	E	1893 - 1926	198 - 231
12	12	chain 'B' and (resid 1927 through 1949 )	B	E	1927 - 1949	232 - 254
13	13	chain 'B' and (resid 1950 through 1968 )	B	E	1950 - 1968	255 - 273

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Yorodumi