PDB-9gua: NCS-1 bound to FDA ligand 5

ID or keywords:

Entry

Database: PDB / ID: 9gua

Title

NCS-1 bound to FDA ligand 5

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 / calcium ion binding / dendrite / perinuclear region of cytoplasm / Golgi apparatus ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

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

Funding support

Spain, 1items

Citation

Journal: To Be Published
Title: NCS-1 bound to FDA ligands
Authors: Munoz-Reyes, D. / Sanchez-Barrena, M.J.

History

Deposition	Sep 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 8, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gua.cif.gz	312.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9gua.ent.gz	214.8 KB	Display	PDB format
PDBx/mmJSON format	9gua.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/gu/9gua ftp://data.pdbj.org/pub/pdb/validation_reports/gu/9gua	HTTPS FTP

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Related structure data

Related structure data	9guzC 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	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

B: Neuronal calcium sensor 1

D: Neuronal calcium sensor 1

hetero molecules

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

1

B: Neuronal calcium sensor 1

hetero molecules

defined by author
24.4 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
24.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.274, 79.611, 148.958
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-350- HOH
2	1	B-356- HOH
3	1	B-482- HOH
4	1	D-384- HOH

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Protein , 1 types, 2 molecules BD

#1: Protein	Neuronal calcium sensor 1 / NCS-1 / Frequenin homolog / Frequenin-like protein / Frequenin-like ubiquitous protein Mass: 21902.668 Da / Num. of mol.: 2 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 , 5 types, 530 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-0LI / 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide / Ponatinib Mass: 532.559 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₉H₂₇F₃N₆O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₄O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.55 Å³/Da / Density % sol: 51.71 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 25 % PEG 3350, 100 mM Bis-Tris pH 5.5, 200 mM sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.592→74.479 Å / Num. obs: 455569 / % possible obs: 93.1 % / Redundancy: 11.1 % / B_iso Wilson estimate: 19.93 Å² / CC_1/2: 0.999 / Net I/σ(I): 16.4
Reflection shell	Resolution: 1.592→1.777 Å / Num. unique obs: 8342 / CC_1/2: 0.644

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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: 1.65→54.7 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 26.8363
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2172	3666	4.78 %
R_work	0.1736	73016	-
obs	0.1757	76682	73.67 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→54.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3008	0	349	503	3860

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0117	3478
X-RAY DIFFRACTION	f_angle_d	1.0002	4726
X-RAY DIFFRACTION	f_chiral_restr	0.0499	449
X-RAY DIFFRACTION	f_plane_restr	0.0083	848
X-RAY DIFFRACTION	f_dihedral_angle_d	14.9406	1478

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 (%)
1.65-1.67	0.4158	20	0.3046	343	X-RAY DIFFRACTION	9.04
1.67-1.69	0.3695	25	0.3276	428	X-RAY DIFFRACTION	11.54
1.69-1.72	0.4451	34	0.3149	649	X-RAY DIFFRACTION	17.1
1.72-1.74	0.225	33	0.315	760	X-RAY DIFFRACTION	19.97
1.74-1.77	0.3568	43	0.2825	979	X-RAY DIFFRACTION	25.52
1.77-1.8	0.2691	53	0.2751	1112	X-RAY DIFFRACTION	29.43
1.8-1.83	0.3051	78	0.2731	1461	X-RAY DIFFRACTION	37.98
1.83-1.87	0.2656	82	0.2696	1737	X-RAY DIFFRACTION	45.9
1.87-1.9	0.3268	118	0.2793	2748	X-RAY DIFFRACTION	70.78
1.9-1.94	0.4902	119	0.4005	2527	X-RAY DIFFRACTION	66.89
1.94-1.98	0.3285	189	0.2412	3761	X-RAY DIFFRACTION	97.97
1.98-2.03	0.216	168	0.2097	3846	X-RAY DIFFRACTION	99.7
2.03-2.08	0.2656	180	0.2118	3799	X-RAY DIFFRACTION	100
2.08-2.14	0.2335	150	0.1837	3845	X-RAY DIFFRACTION	100
2.14-2.2	0.2346	199	0.1758	3830	X-RAY DIFFRACTION	100
2.2-2.27	0.2611	169	0.26	3200	X-RAY DIFFRACTION	84.61
2.27-2.35	0.2075	187	0.1685	3807	X-RAY DIFFRACTION	100
2.35-2.44	0.1978	218	0.1662	3768	X-RAY DIFFRACTION	100
2.44-2.56	0.232	174	0.1596	3829	X-RAY DIFFRACTION	100
2.56-2.69	0.2264	200	0.1641	3788	X-RAY DIFFRACTION	99.97
2.69-2.86	0.2302	204	0.17	3832	X-RAY DIFFRACTION	100
2.86-3.08	0.2386	178	0.1639	3818	X-RAY DIFFRACTION	100
3.08-3.39	0.2103	264	0.1461	3740	X-RAY DIFFRACTION	100
3.39-3.88	0.1704	196	0.1379	3788	X-RAY DIFFRACTION	99.7
3.88-4.89	0.142	151	0.1257	3840	X-RAY DIFFRACTION	99.87
4.89-54.7	0.2003	234	0.1609	3781	X-RAY DIFFRACTION	99.9

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	6.67945229498	1.52172379776	-0.406365852772	2.05580235739	2.74307997426	6.01248775873	0.0670155957086	0.50229291632	1.71340435001	-0.467083662633	0.186149239981	-0.474591890694	-0.823070480747	0.12910464789	-0.253603287132	0.233441111966	0.00482663155537	0.00188447985286	0.225314031992	0.0915079320263	0.5794499496	-17.2074223027	16.8854549085	20.8654148182
2	2.04746616037	3.99977207696	2.5607647577	4.73627208242	0.965864355353	3.73809711564	-0.0874562078538	-1.52260146388	1.14750898439	0.509493272619	0.273202203424	-0.575071652018	-0.277327785175	0.208978920718	-0.101302064717	0.250238225205	0.0344712997754	-0.0874232555674	0.353932763825	-0.221563517348	0.572757906123	-12.2897112216	15.9156710831	30.3512226494
3	2.33059255805	0.450958641122	-1.89230328453	8.14961773719	0.539519666732	1.76380382996	0.120625617186	-0.712171568408	1.36977092032	0.132542460021	0.00520409549717	-0.0398982514662	-0.399219388597	0.127690613804	-0.109507893833	0.226256165813	0.00738545498506	-0.0596960940782	0.253704657921	-0.163004491872	0.626095170225	2.3805671111	12.3233676925	29.1618711076
4	4.45662667593	-1.55362757854	2.31002649609	2.55915908551	-1.48724348759	6.40948681463	0.0857910598848	0.019742052521	0.470475313019	0.260468509612	-0.146418955945	-0.426073006593	-0.0192866334863	0.471366672062	0.0661245932545	0.15047499056	-0.0201972056755	-0.0410915287627	0.142680316172	-0.0689139178595	0.293569993522	5.04467088645	3.38900953688	25.4198315389
5	5.92311370363	3.1525921446	-0.892176108167	4.8302872084	-0.779122045511	1.89637941184	0.0738568976581	0.228501672401	1.07497848977	-0.088551080504	-0.0585794623339	-0.230725597927	-0.345489033297	0.128750511647	0.0145982522432	0.168937914815	-0.00341985475207	0.00267654051368	0.153803174253	0.020334728234	0.491398985527	-5.51263792392	11.7533190467	19.7874179243
6	7.92125507543	-1.54162394675	-5.05744209929	4.50228944119	1.55631544748	4.37806402426	0.0676479109029	0.52276075067	-0.0409376468782	-0.260892798492	-0.187793896315	0.149480692365	-0.0802377572221	-0.177371572404	0.105926968738	0.147191012483	0.00643267948326	-0.0175216089332	0.170747937747	0.00301917501119	0.156712802769	-6.71557082355	-1.76476373796	14.6489488928
7	3.00525815202	0.91115814652	1.28981473169	4.43322426364	-0.047735281756	1.99686815232	-0.0217922373814	0.208174457136	-0.262831792153	-0.250134262923	0.0737156750341	-0.707878904312	0.151559273805	0.226271514858	-0.0441938680277	0.127946861126	0.00597450364866	0.0446337165408	0.195630868962	-0.0464201868948	0.285424933461	5.22995585219	-10.5437047588	16.371939792
8	4.47650851383	-1.52849788007	-2.08115125589	7.69410377006	3.18760741575	4.30442261635	-0.149610596444	0.0829194169635	-0.0835631962937	0.000520374514829	-0.0282117258365	0.152596479432	0.0414708427925	-0.0196744475923	0.198011843397	0.0479086512227	0.00323169939887	-0.0498348230908	0.125753545022	-0.00406060956621	0.126063383602	-9.18981485085	-7.77766312627	18.8566027176
9	2.06624193551	-0.126090363253	2.00021037782	6.49575420621	-0.572918415925	6.44510389508	0.17605069713	-0.4518027358	0.0218588074773	0.0786476366881	-0.12265925105	1.32053702916	-0.00171404002216	-1.06262132525	-0.0920528503336	0.180510361641	0.00123918402484	0.0372126812544	0.297238897068	-0.0797704864547	0.384066501641	18.9828003715	18.2507676748	15.7559651794
10	7.40973345949	6.58526061909	2.29855678892	2.07950743274	4.79290374445	4.33331932001	-0.317767010605	0.4843414433	0.119085197345	-0.8965332068	0.227395808504	0.36561311942	-0.257379773091	-0.00233946722625	0.0786408566147	0.237018441681	-0.00716244537484	-0.0423801494798	0.242593279984	-0.00542570607341	0.189278649339	19.7709252001	12.7115255597	7.16767778651
11	2.08237578509	-0.77225127678	-1.40823332553	1.68280753738	-0.688539247686	0.809812685069	-0.0110978750516	0.348685183437	-0.38627432365	-0.25464767809	-0.056841079462	0.209715562743	0.0410538088774	-0.073049662344	0.0299318894853	0.172348757374	-0.0145200562173	-0.0344488274656	0.195394533815	-0.0413197477111	0.136655578216	22.8306774111	-1.94545776058	8.32401811855
12	3.33888667543	-0.65766365549	-0.273356961603	3.1920114823	0.768847157692	5.92046661059	0.0203603773774	0.0387376856518	-0.419819725284	-0.0971077196192	0.0684010053875	0.139727849145	0.360377011955	0.159972312175	-0.0954732171565	0.133021131623	-0.00951099330213	-0.0329511256406	0.117382675801	-0.0137773682057	0.132464980804	31.7647415682	-4.86561471803	11.6399397362
13	6.69694635944	1.51942857652	0.194720037426	5.02516163621	-0.642486271116	1.7924282757	-0.0931433128963	-0.548996527788	-0.0163436073146	0.295063248774	0.0229243783217	0.321477595395	0.0542829795197	-0.161565167086	0.0410311649133	0.144288080333	0.000283558080767	0.0253835868757	0.190169456117	-0.0268316010133	0.0864201239819	23.7626513921	5.86947007867	17.7919055687
14	2.81616893007	-1.26496913185	0.877311747853	6.35633490012	-4.31128343468	4.73099500915	-0.00307402458417	-0.579768469698	-0.00555343490058	0.483091382695	0.000764855647754	0.173253080423	-0.0225954922573	-0.150479122801	0.012950422793	0.168510342501	-0.0208655766963	0.00185048369861	0.217117598873	-0.01328623788	0.0860846405994	37.2656441419	2.46351772055	25.1910615814
15	6.70970808625	-0.428893000087	0.168542144814	5.68401743227	-0.26626072589	2.08096426634	0.0469568088185	0.0911898431345	-0.573630383288	-0.406987473677	-0.152601092901	-0.129425456455	0.402292985611	0.153086007016	0.101210606155	0.167210085688	0.00212519940535	0.0146829454657	0.110771720246	-0.0223524997998	0.198468473825	41.5333453544	-7.90215504724	14.7446982917
16	6.11322847177	0.804341862314	1.19696628697	5.69051263008	3.71446144694	7.50033947757	0.123191789499	0.275093692483	-0.675945567168	-0.209012373883	0.164716940563	-0.374170324479	0.177457977342	0.188476363141	-0.265742536673	0.155391716173	0.0173680293411	-0.0343330009787	0.134547446097	-0.018769686698	0.238321774084	51.49573485	-6.3650968453	16.3298729508
17	3.98410431538	-4.05804479963	4.08699990227	7.71235593418	-0.20317293361	8.58061150048	0.127975731493	-1.15306216372	-0.751790812931	1.04364350407	-0.0247660180815	-0.238122249422	0.350818978176	0.122099378564	-0.104970138955	0.278078632587	-0.0398276529193	-0.046119438853	0.411143332907	0.11982798161	0.205627809325	48.2882680488	-2.93923033672	32.7830145902
18	8.20400634929	3.97186794792	-5.96711996044	8.74224482303	-4.13626299501	8.08393569868	0.367932599165	-0.511223106201	0.671501848013	0.848516275354	-0.129805746125	0.193383957673	-0.78747803592	-0.0473404471301	-0.178476838529	0.23419846886	-0.00344937109832	-0.0169442321024	0.203493012632	-0.0493518929884	0.157060045704	45.7817083627	5.97576296694	27.4367293392
19	2.2002874078	-4.30092690059	8.11964171212	6.67785108855	-1.36150735573	8.50893442757	0.22015078719	0.616297578473	0.616524084251	-0.539581277398	-0.433572603847	-0.236907971563	0.0726384649699	0.355084175561	0.230595103202	0.196798236352	0.0169433865677	0.0552501964429	0.186129716508	0.0578392142437	0.145624966613	42.8215736999	10.2765744053	12.0900773062

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 23 )	B	D	7 - 23	1 - 17
2	2	chain 'B' and (resid 24 through 37 )	B	D	24 - 37	18 - 31
3	3	chain 'B' and (resid 38 through 55 )	B	D	38 - 55	32 - 49
4	4	chain 'B' and (resid 56 through 72 )	B	D	56 - 72	50 - 66
5	5	chain 'B' and (resid 73 through 94 )	B	D	73 - 94	67 - 88
6	6	chain 'B' and (resid 95 through 108 )	B	D	95 - 108	89 - 102
7	7	chain 'B' and (resid 109 through 165 )	B	D	109 - 165	103 - 159
8	8	chain 'B' and (resid 166 through 190 )	B	D	166 - 190	160 - 184
9	9	chain 'D' and (resid 6 through 23 )	D	H	6 - 23	1 - 18
10	10	chain 'D' and (resid 24 through 37 )	D	H	24 - 37	19 - 32
11	11	chain 'D' and (resid 38 through 55 )	D	H	38 - 55	33 - 50
12	12	chain 'D' and (resid 56 through 72 )	D	H	56 - 72	51 - 67
13	13	chain 'D' and (resid 73 through 94 )	D	H	73 - 94	68 - 89
14	14	chain 'D' and (resid 95 through 117 )	D	H	95 - 117	90 - 112
15	15	chain 'D' and (resid 118 through 135 )	D	H	118 - 135	113 - 130
16	16	chain 'D' and (resid 136 through 156 )	D	H	136 - 156	131 - 151
17	17	chain 'D' and (resid 157 through 165 )	D	H	157 - 165	152 - 160
18	18	chain 'D' and (resid 166 through 174 )	D	H	166 - 174	161 - 169
19	19	chain 'D' and (resid 175 through 190 )	D	H	175 - 190	170 - 185

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