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- PDB-9guz: NCS-1 bound to FDA ligand 2 -

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Basic information

Entry
Database: PDB / ID: 9guz
TitleNCS-1 bound to FDA ligand 2
ComponentsNeuronal calcium sensor 1
KeywordsMETAL 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 ...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 / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Recoverin family / EF hand domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / ACETIC ACID / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMunoz-Reyes, D. / Sanchez-Barrena, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-137331OB-C31 Spain
CitationJournal: To Be Published
Title: NCS-1 bound to FDA ligands
Authors: Munoz-Reyes, D. / Sanchez-Barrena, M.J.
History
DepositionSep 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Neuronal calcium sensor 1
A: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,27017
Polymers43,8052
Non-polymers2,46515
Water1,08160
1
B: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2549
Polymers21,9031
Non-polymers1,3528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0168
Polymers21,9031
Non-polymers1,1137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.139, 55.738, 76.686
Angle α, β, γ (deg.)90.000, 94.400, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules BA

#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 (E. coli) / References: UniProt: P62166

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Non-polymers , 7 types, 75 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-A1IO4 / ethyl 3-[[2-[[[4-(~{N}'-hexoxycarbonylcarbamimidoyl)phenyl]amino]methyl]-1-methyl-benzimidazol-5-yl]carbonyl-pyridin-2-yl-amino]propanoate


Mass: 627.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H41N7O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate trihydrate pH 6.5, 0.2 M sodium acetate trihydrate, 30% (v/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.921 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.28→76.46 Å / Num. obs: 59870 / % possible obs: 90.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.77 Å2 / CC1/2: 0.98 / Net I/σ(I): 5.3
Reflection shellResolution: 2.285→2.626 Å / Num. unique obs: 3237 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1-5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→54.98 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2587 541 5.18 %
Rwork0.2086 9912 -
obs0.2113 10453 49.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.47 Å2
Refinement stepCycle: LAST / Resolution: 2.28→54.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 159 60 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473184
X-RAY DIFFRACTIONf_angle_d0.73954265
X-RAY DIFFRACTIONf_chiral_restr0.0384432
X-RAY DIFFRACTIONf_plane_restr0.0077555
X-RAY DIFFRACTIONf_dihedral_angle_d15.9511458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.510.311160.2882260X-RAY DIFFRACTION5.03
2.52-2.880.3304520.27421160X-RAY DIFFRACTION22.99
2.88-3.630.30071930.22963393X-RAY DIFFRACTION67.65
3.63-54.980.23322900.1915099X-RAY DIFFRACTION99.72
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.3601709739-0.470642980903-0.3640580757063.552055849910.6361805039932.318235318870.2339219151180.2053432307420.090265522394-0.4541055964130.00253248540922-0.4689550462410.2483765511430.56633483754-0.1487214858820.1851995798720.03807620159450.01328888135540.2144710335810.0371538233130.22954399329911.5558220008-32.439435945830.9412038906
22.21764980499-1.15725166459-1.24174071442.887702824491.649073479931.13439365129-0.2745765313310.302164309313-0.215534901874-0.610487238446-0.169869039066-0.0219226819391-0.1933680090540.08346451816520.1514574906150.4951144870050.1783929991050.1616634906590.365035115539-0.06355651340930.4844075063120.8101321756-16.775222374226.0665202694
31.650738385340.2886028038490.5121169216532.31507379511.40731791931.36242291255-0.1783103178530.0376562332261-0.0521650643613-0.4607273181850.0725929029211-0.4569606308910.3535233681160.09775037583210.03255823016070.0141164577770.08260495549690.01162825268640.1331124939440.05166279823120.31210455944313.4243412722-14.191292154637.251121843
42.83883404661-1.25897080725-1.224749220394.456706855340.8885716089040.6179808702220.1080195227530.7705416156230.397159587794-1.20774915403-0.2988253648960.0915648966553-0.879310836513-0.4008118949010.09215691073090.233927932670.169459039970.05774684006590.237770630427-0.01897306243460.3989857180610.31167965593.4881253843931.6785859136
51.34410603693-0.921369093477-0.3685246422322.30009837677-3.346257947957.6478759712-0.07204125663590.04754916565290.081676307023-0.0180440458083-0.0820834959276-0.302403736659-0.4407532369870.2605500675330.142790319075-0.1502472001870.223921161508-0.6723809022130.1898515056120.034917185585-0.4081187474514.842002703424.6265183547740.6203671637
61.472219926360.627816600380.4604193347663.296303181481.275223140021.11057578451-0.178434578839-0.02307925284910.0399124863793-0.0612509072516-0.1696581902530.1695964432750.009066294232880.07639655098870.2110938766340.135712971621-0.0123993182427-0.005672867040310.09835034833080.0475498796040.1784045984720.535923444179-6.9349198202842.2302505047
72.31180094971.079032075920.8310801648662.480947153550.9761052869964.10280052972-0.09354180027090.165840637255-0.261731124256-0.2149811335820.04104184838580.6173199152780.151790152446-0.07364349082330.05852386591950.336097650630.0684118242548-0.1003262717880.173556660696-0.03457221458680.34020739220612.3794384188-42.072941928962.7098006797
80.8636945043212.38920152570.9102895328287.029219847621.719923416241.730228147890.4021132081990.406798712075-0.322073867315-0.3374601880810.132483882450.5129027462940.55839851377-0.265141799917-0.1653887994280.449907293505-0.134126009501-0.2286410807260.430587519685-0.009570848395580.4628248399147.07221040547-27.038044130753.3694688768
92.52264902749-0.2097300900582.610904244836.33825444924-1.693348924663.01692809119-0.0823592633079-0.140911534041-0.01573287460510.09797483774670.1369033346390.8269673690920.137705085931-0.36210102887-0.01726344664270.375738849026-0.091724050034-0.01624021946880.225697895688-0.001223162833040.04977578661839.70637198553-19.001851823757.839490776
105.400075884270.641500844024-6.016769435438.94534597079-4.004990230037.89847941171-0.1827072633390.489659715698-0.0789944238421-0.590129015645-0.1717653968230.162013889556-0.0725980678371-0.1025747261650.04326707341331.237644257860.369842161825-0.1257132605650.46436155067-0.2046381179130.022742192863218.5470470416-31.005255107851.3919128774
110.3842928881030.665370971568-0.3050513074292.20135421088-0.6142841665910.572432994635-0.01438747740320.176111994652-0.0145619737726-0.605297433282-0.02997137157150.044977128930.1500286424090.1958831721720.05872688364880.3454730703540.0297438442465-0.0392500931740.198587608690.03935244667450.13889162316922.1154178062-25.021851688563.9468321855
122.74866631660.3998527631191.572163052672.241606078550.2847786580952.38961688242-0.000439966324988-0.1689633952950.301315007564-0.0201693335981-0.261379337503-0.103939523456-0.3711269017840.1437343203530.2856624381290.204548025125-0.0177358681136-0.01185032446410.2011692855060.06102409175830.14864169464120.9971557342-6.7821674674465.4539158335
130.08820424483860.372560440699-0.1916803047643.909022471510.3327581835022.049520528980.00619479138181-0.163145511434-0.1706525557560.357569708331-0.225473130243-0.001603957862790.369822104747-0.03457792170370.2863237780850.3920922612730.0217855081766-0.03059959150210.2809258359560.0112771430030.15363431233621.9428344326-19.635208006574.8890998745
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 6 through 37 )BA6 - 371 - 32
22chain 'B' and (resid 38 through 55 )BA38 - 5533 - 50
33chain 'B' and (resid 56 through 117 )BA56 - 11751 - 112
44chain 'B' and (resid 118 through 144 )BA118 - 144113 - 139
55chain 'B' and (resid 145 through 156 )BA145 - 156140 - 151
66chain 'B' and (resid 157 through 189 )BA157 - 189152 - 184
77chain 'A' and (resid 6 through 38 )AJ6 - 381 - 33
88chain 'A' and (resid 39 through 53 )AJ39 - 5334 - 48
99chain 'A' and (resid 54 through 72 )AJ54 - 7249 - 67
1010chain 'A' and (resid 73 through 81 )AJ73 - 8168 - 76
1111chain 'A' and (resid 82 through 117 )AJ82 - 11777 - 112
1212chain 'A' and (resid 118 through 165 )AJ118 - 165113 - 156
1313chain 'A' and (resid 166 through 189 )AJ166 - 189157 - 180

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