PDB-9gu6: NCS-1 bound to FDA ligand 3

ID or keywords:

Entry

Database: PDB / ID: 9gu6

Title

NCS-1 bound to FDA ligand 3

Components

Neuronal calcium sensor 1

Keywords

METAL BINDING PROTEIN / Neuronal calcium sensor 1 / EF-hand containing protein / drug repurposing / FDA ligand

Function / homology

Function and homology information

calcium sensitive guanylate cyclase activator activity / regulation of neuron projection development / regulation of signal transduction / voltage-gated calcium channel activity / postsynaptic density / axon / intracellular membrane-bounded organelle / calcium ion binding / dendrite / perinuclear region of cytoplasm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Munoz-Reyes, D. / Sanchez-Barrena, M.J.

Funding support

Spain, 1items

Citation

Journal: J.Med.Chem. / Year: 2025
Title: FDA Drug Repurposing Uncovers Modulators of Dopamine D 2 Receptor Localization via Disruption of the NCS-1 Interaction.
Authors: Munoz-Reyes, D. / Aguado, L. / Arroyo-Urea, S. / Requena, C. / Perez-Suarez, S. / Sanchez-Yepes, S. / Argerich, J. / Miro-Rodriguez, C. / Ulzurrun, E. / Rodriguez-Martin, E. / Garcia-Nafria, ...

History

Deposition	Sep 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gu6.cif.gz	558.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9gu6.ent.gz	385.1 KB	Display	PDB format
PDBx/mmJSON format	9gu6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gu6_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	9gu6_full_validation.pdf.gz	2.2 MB	Display
Data in XML	9gu6_validation.xml.gz	44.7 KB	Display
Data in CIF	9gu6_validation.cif.gz	57.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/9gu6 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/9gu6	HTTPS FTP

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Related structure data

Related structure data	9gtoC 9gu8C 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	#96 - Dec 2007 Oxidosqualene Cyclase similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

B: Neuronal calcium sensor 1

D: Neuronal calcium sensor 1

F: Neuronal calcium sensor 1

H: Neuronal calcium sensor 1

hetero molecules

94 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Neuronal calcium sensor 1

hetero molecules

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

2

D: Neuronal calcium sensor 1

hetero molecules

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

3

F: Neuronal calcium sensor 1

hetero molecules

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

4

H: Neuronal calcium sensor 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.290, 59.624, 65.448
Angle α, β, γ (deg.)	87.360, 89.960, 85.060
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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Protein , 1 types, 4 molecules BDFH

#1: Protein	Neuronal calcium sensor 1 / NCS-1 / Frequenin homolog / Frequenin-like protein / Frequenin-like ubiquitous protein Mass: 21902.668 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCS1, FLUP, FREQ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P62166

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Non-polymers , 8 types, 590 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-117 / 7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID / ATORVASTATIN Mass: 558.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₃H₃₅FN₂O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₂O₄
#6: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₄O₂
#7: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₄H₆O₄
#8: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.81 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 70% (v/v) Tacsimate pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 29, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.968 Å / Relative weight: 1
Reflection	Resolution: 1.928→65.378 Å / Num. obs: 131978 / % possible obs: 84.3 % / Redundancy: 3.1 % / B_iso Wilson estimate: 8.42 Å² / CC_1/2: 0.787 / Net I/σ(I): 4.3
Reflection shell	Resolution: 1.928→2.117 Å / Num. unique obs: 8325 / CC_1/2: 0.588

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Processing

Software

Name	Version	Classification
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing
PHENIX	1.21.1-5286	refinement
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→24.7 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.7131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.256	4118	4.93 %
R_work	0.2191	79334	-
obs	0.2209	83452	66.57 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.74 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→24.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5909	0	425	540	6874

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6456
X-RAY DIFFRACTION	f_angle_d	0.5786	8682
X-RAY DIFFRACTION	f_chiral_restr	0.0381	881
X-RAY DIFFRACTION	f_plane_restr	0.0131	1149
X-RAY DIFFRACTION	f_dihedral_angle_d	17.1003	2404

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 (%)
1.93-1.95	0.5801	4	0.3697	118	X-RAY DIFFRACTION	2.85
1.95-1.97	0.2942	8	0.4064	315	X-RAY DIFFRACTION	7.45
1.98-2	0.3645	22	0.3274	296	X-RAY DIFFRACTION	7.52
2-2.03	0.432	17	0.3214	437	X-RAY DIFFRACTION	10.63
2.03-2.05	0.3186	18	0.3175	569	X-RAY DIFFRACTION	13.33
2.05-2.08	0.4055	31	0.3172	749	X-RAY DIFFRACTION	18.85
2.08-2.11	0.3203	74	0.3241	1307	X-RAY DIFFRACTION	31.72
2.11-2.15	0.3234	97	0.304	1757	X-RAY DIFFRACTION	42.94
2.15-2.18	0.3473	91	0.2906	2275	X-RAY DIFFRACTION	55.38
2.18-2.22	0.3058	107	0.2748	2772	X-RAY DIFFRACTION	65.37
2.22-2.26	0.3173	188	0.2665	2994	X-RAY DIFFRACTION	74.42
2.26-2.3	0.2935	182	0.2699	3331	X-RAY DIFFRACTION	80.8
2.3-2.35	0.3103	212	0.2674	3557	X-RAY DIFFRACTION	86.96
2.35-2.4	0.2922	206	0.2675	3570	X-RAY DIFFRACTION	87.65
2.4-2.46	0.2967	169	0.2658	3592	X-RAY DIFFRACTION	88.04
2.46-2.52	0.2627	165	0.2592	3694	X-RAY DIFFRACTION	86.68
2.52-2.59	0.2652	171	0.2462	3400	X-RAY DIFFRACTION	83.83
2.59-2.66	0.327	196	0.234	3294	X-RAY DIFFRACTION	81.66
2.66-2.75	0.2844	148	0.2317	2915	X-RAY DIFFRACTION	71.1
2.75-2.85	0.2936	132	0.2214	2902	X-RAY DIFFRACTION	69.21
2.85-2.96	0.265	195	0.2141	3707	X-RAY DIFFRACTION	90.07
2.96-3.1	0.2587	203	0.2018	3971	X-RAY DIFFRACTION	97.34
3.1-3.26	0.2068	200	0.1934	3992	X-RAY DIFFRACTION	97.04
3.26-3.46	0.2303	227	0.1784	3992	X-RAY DIFFRACTION	96.94
3.46-3.73	0.227	152	0.1763	4029	X-RAY DIFFRACTION	96.74
3.73-4.1	0.1796	223	0.1565	3959	X-RAY DIFFRACTION	97.57
4.1-4.69	0.1732	247	0.1565	3970	X-RAY DIFFRACTION	97.3
4.69-5.9	0.2474	294	0.1969	3919	X-RAY DIFFRACTION	97.79
5.9-24.7	0.2814	139	0.2147	3951	X-RAY DIFFRACTION	94.54

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	6.79835248731	-4.44613352494	-0.543068771943	2.00120161649	-1.32484211749	4.06367394252	0.0932172268909	0.220671069987	-0.0782167672683	-0.417433442683	-0.0706739883352	-0.644771362463	0.506198395657	0.403297781301	-0.0521856404729	0.219085323659	-0.0323837025844	0.00879996437834	0.108135926392	-0.189387875284	0.224421192178	36.5718769478	10.4119851938	5.75431574288
2	2.65801666435	-0.413714364703	-0.335001659653	2.09300418217	0.0994050562219	1.1749295011	0.0335590902584	-0.28861584674	-0.548314346136	0.173446596536	0.0773572687328	-0.00282141541797	0.332792621733	-0.0298209283134	-0.0898397199381	0.12662509744	0.0212366000434	-0.0419435687783	0.0920279968951	0.02655686569	0.105751198256	22.7603826323	4.96453764892	13.9472054208
3	1.67459597869	0.0502155123053	0.175231514002	1.582900588	0.574246488999	0.503610733473	-0.102342664153	0.201981782931	-0.3380130901	-0.0947093633488	0.0171656901857	-0.010674092806	0.0383925633091	-0.0500278837906	0.0130906753093	0.0020371477239	0.0711033214981	-0.0361397688433	0.0137379280817	-0.0602248904349	0.0899171275968	17.8269812249	6.83841110482	5.37965165725
4	2.97136464575	0.0345156859099	-0.445751488881	2.56786867462	-0.191947982361	1.11613617723	-0.0629224042033	-0.128320623232	-0.0439850776612	0.0243877120814	0.0050372705179	0.182153467827	-0.0548567115246	-0.12380306706	0.0537066921436	0.0273199336321	0.0244922009032	-0.0126620134284	0.0789657514757	-0.0825372619006	0.0746418974997	3.39930419994	13.7548038622	4.10122068275
5	3.09722985487	-0.0592538904705	1.42872881883	0.959087094586	-0.114793923817	1.72240481487	-0.0428613863945	0.0237137025944	0.191868584483	0.0402354614207	-0.0360982946276	0.0363542343106	-0.0994016696874	0.00476137513585	0.0840994692749	0.0886536854563	0.0632322866863	-0.0298746747012	0.0935678134609	-0.0351146515527	0.0311740855301	3.7926938846	22.6785858919	2.50666470254
6	7.20098345425	2.66434699169	-2.44443825653	8.86304998427	1.78645578268	6.20630581905	0.181067196783	-0.333941404961	0.199882070493	0.49918144578	0.0312245865057	-0.463061152495	-0.362092945528	0.42001580014	-0.222011053085	0.0919831966466	0.103790073018	-0.0270137517098	0.18428236951	-0.214108869956	0.184863319266	58.9122035276	-17.7571169702	9.31578357218
7	4.04336336958	-1.93888597798	0.806448135883	2.32493294419	-0.221644009875	0.739958532323	-0.019939273092	0.300591582595	0.579144087775	-0.143047699975	0.00622051730459	-0.254679857063	-0.361888288459	0.0812723834565	0.0268798866581	0.110008094625	0.0263249736522	0.0183318834615	0.133970222198	0.0393852918634	0.163220683077	45.2106299007	-12.3887294175	1.16398999191
8	1.94042884475	-0.780119361158	-0.364987364186	1.6907869309	0.208608718983	0.689789787943	0.0116572747553	-0.221397247107	0.202251181809	0.231528260561	-0.00210814307617	-0.129368929655	-0.128122831136	0.0572266644837	-0.0173299536838	0.0277450241194	-0.0156450139315	-0.00139421273506	0.00845368744412	-0.0613724108004	0.0784086646361	40.3574483639	-14.301210808	9.59364825824
9	3.41743990425	0.0253356642094	0.393736486655	2.69104079207	-0.0297486250431	1.5854612147	-0.00451040359741	0.127632283987	0.0506520221277	-0.0712380625953	0.0296970617489	0.0520847609394	0.00540800651329	-0.0943185520283	-0.0159202242235	0.0414390604658	0.00448783729269	-0.0164816594218	0.0509763982617	-0.0295075987019	-0.00415219079563	25.965475412	-21.2275557189	10.932868131
10	2.35290592464	0.438970621585	-0.205834185645	1.4080559292	0.16033385944	0.856410404057	-0.0182939517405	0.0652021395835	-0.21100066064	-0.0192356902637	-0.0455354133839	0.0518517360395	0.170162908984	-0.0121221124622	0.0586876577693	0.0762105347659	-0.0204892791455	0.00126222897692	0.0446107395311	-0.0381580111543	0.0741393952082	26.3334933283	-30.0524567481	12.4984002063
11	2.00090804537	8.66490141519	6.98430239766	9.66807784587	7.24093940832	9.91718345744	0.20365775271	-0.996054060954	-0.631688884134	0.747762718465	-0.282903878569	0.983281414218	0.51344980893	-0.991795335839	0.0908631981445	0.26759169122	0.123630270665	0.157715369904	0.460820039821	0.279429811167	0.739654605876	-12.4692754593	8.72743883396	-23.8204789026
12	4.90736155249	-2.09719058313	-0.522402379318	1.99069454998	0.376860786279	0.648913206159	0.175913717834	0.404848832771	-1.0669097626	-0.149206694977	-0.243227291982	0.723605331979	0.314311818391	-0.153509507489	0.0590978657561	0.180359817886	0.0159833831993	-0.0808234401911	0.241748347167	-0.0284771658401	0.448119787936	1.29453268926	3.3235105252	-32.3970531461
13	3.30302317443	-0.84988888386	1.60148686137	3.79147341805	-0.726787209903	0.920950130452	0.0363040585765	-0.18631547067	-0.611861805094	0.350400756752	0.11751113575	0.499032024701	0.110992189508	-0.0528645880429	-0.119289969414	0.103403644722	-0.0201890378982	0.0224198543168	0.159452107263	0.086347888525	0.227528696126	6.35997629919	5.29156249172	-24.1240391315
14	1.59924658359	-0.537763432961	0.123785659875	1.57125904317	0.532276289979	2.942659152	0.082315488488	0.11581758061	0.00782260962318	-0.228144218153	-0.017258597913	-0.309360188098	0.0497785905995	0.339234645968	-0.0173477345977	0.223975978824	0.0877578448437	0.028930081833	0.135723053026	0.105760956212	-0.0762908128257	19.7612513378	11.3227449307	-21.2614208272
15	5.12584387421	-0.737261982013	0.0490211201765	1.96447358224	-0.616764190425	0.220303306581	-0.053270863193	0.293409627014	0.12636539798	-0.122816690888	-0.118183911022	-0.0513415693671	0.0281554766696	0.234681953071	0.126163798393	0.171721882167	0.00720117810341	0.0433842743652	0.20214531119	-0.0510326785321	0.0310484000625	20.4948314111	20.4747287314	-20.8244492068
16	2.00153059155	-3.88601752774	1.06100777509	2.00082994035	-0.0752379712685	0.762072894203	0.281272569093	0.584492534582	0.361995498068	-0.806149359245	-0.377551081533	0.653422359339	-0.777456882946	-0.843815785993	0.108384059145	0.328984683533	0.172875312569	-0.0695077738578	0.393812585837	0.158222122072	0.533195289516	9.90087369743	-19.2592208462	-26.1452905093
17	4.14664938034	1.19838190668	0.882862339115	2.56954704752	0.1349882333	0.545230718456	0.0476834881013	-0.427841185161	0.87249114652	0.108481513015	-0.00898248538101	0.586127627799	-0.276086341992	-0.237461616213	-0.0251696648271	0.204482610492	0.0528456970873	0.0704600132191	0.21740829406	-0.0419359852242	0.283176001149	23.7869891167	-13.7771234154	-17.8707071216
18	3.06929221967	0.331679884561	-0.853425672176	2.22286202316	-0.0956350854441	2.05965689763	0.0461055472076	0.216252066211	0.452229383246	-0.194132616232	0.121296641012	0.165550317321	-0.446764689661	-0.192370986364	-0.0839036464415	0.164284381084	0.0435612061815	-0.114150353904	0.104857430737	0.0636191703918	0.188315460108	28.9741767992	-15.6038570348	-26.1879342306
19	2.48963521088	1.2375786259	-0.159413617808	2.55867883031	1.37539012924	2.97436555964	-0.0139836390995	-0.264281569737	-0.0666747543419	0.278827988354	-0.0498461945554	-0.445670114105	-0.0569869450293	0.429590280831	-0.0416103161227	0.155991434089	-0.0587827975341	-0.0638363056435	0.183879807858	0.0169282834917	-0.0767607639157	42.9161409794	-22.029238426	-28.0943778311
20	5.8822816062	0.894064079975	-0.241728141765	1.25514566996	-0.435904130374	0.148243769664	-0.0390236655567	-0.397169477736	-0.085849987935	0.0951496184622	-0.00464580029194	0.0158599094242	-0.0120033614381	0.261921295728	0.0463912467894	0.117683494367	0.0218914299915	-0.0468801169884	0.158859876786	-0.0419979231643	0.0976757267947	42.936130837	-30.85727297	-29.5237301506

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 'B' and (resid 7 through 19 )	B	D	7 - 19	2 - 14
2	2	chain 'B' and (resid 20 through 58 )	B	D	20 - 58	15 - 53
3	3	chain 'B' and (resid 59 through 96 )	B	D	59 - 96	54 - 91
4	4	chain 'B' and (resid 97 through 144 )	B	D	97 - 144	92 - 139
5	5	chain 'B' and (resid 145 through 189 )	B	D	145 - 189	140 - 184
6	6	chain 'D' and (resid 7 through 19 )	D	H	7 - 19	2 - 14
7	7	chain 'D' and (resid 20 through 58 )	D	H	20 - 58	15 - 53
8	8	chain 'D' and (resid 59 through 96 )	D	H	59 - 96	54 - 91
9	9	chain 'D' and (resid 97 through 144 )	D	H	97 - 144	92 - 139
10	10	chain 'D' and (resid 145 through 189 )	D	H	145 - 189	140 - 184
11	11	chain 'F' and (resid 7 through 19 )	F	L	7 - 19	1 - 13
12	12	chain 'F' and (resid 20 through 58 )	F	L	20 - 58	14 - 52
13	13	chain 'F' and (resid 59 through 96 )	F	L	59 - 96	53 - 90
14	14	chain 'F' and (resid 97 through 144 )	F	L	97 - 144	91 - 131
15	15	chain 'F' and (resid 145 through 189 )	F	L	145 - 189	132 - 176
16	16	chain 'H' and (resid 7 through 19 )	H	P	7 - 19	1 - 13
17	17	chain 'H' and (resid 20 through 58 )	H	P	20 - 58	14 - 52
18	18	chain 'H' and (resid 59 through 96 )	H	P	59 - 96	53 - 90
19	19	chain 'H' and (resid 97 through 144 )	H	P	97 - 144	91 - 134
20	20	chain 'H' and (resid 145 through 189 )	H	P	145 - 189	135 - 179

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