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- PDB-7nx0: LTK:ALKAL1 complex stabilized by a Nanobody -

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Basic information

Entry
Database: PDB / ID: 7nx0
TitleLTK:ALKAL1 complex stabilized by a Nanobody
Components
  • ALK and LTK ligand 1
  • Leukocyte tyrosine kinase receptor
  • Nb3.16
KeywordsPROTEIN BINDING / Cell Surface Receptor Cytokine binding Cytokine receptor complex
Function / homology
Function and homology information


positive regulation of ERK5 cascade / receptor signaling protein tyrosine kinase activator activity / Signaling by LTK / regulation of neuron differentiation / Signaling by ALK / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cardiac muscle cell apoptotic process / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to retinoic acid ...positive regulation of ERK5 cascade / receptor signaling protein tyrosine kinase activator activity / Signaling by LTK / regulation of neuron differentiation / Signaling by ALK / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cardiac muscle cell apoptotic process / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to retinoic acid / transmembrane receptor protein tyrosine kinase activity / cytokine activity / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / positive regulation of neuron projection development / regulation of cell population proliferation / protein tyrosine kinase activity / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / protein phosphorylation / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular region / ATP binding / membrane / plasma membrane
Similarity search - Function
ALK and LTK ligand 1/2 / ALK and LTK ligand 1/2 / Glycine rich protein / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site ...ALK and LTK ligand 1/2 / ALK and LTK ligand 1/2 / Glycine rich protein / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Leukocyte tyrosine kinase receptor / ALK and LTK ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDe Munck, S. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Nature / Year: 2021
Title: Structural basis of cytokine-mediated activation of ALK family receptors.
Authors: De Munck, S. / Provost, M. / Kurikawa, M. / Omori, I. / Mukohyama, J. / Felix, J. / Bloch, Y. / Abdel-Wahab, O. / Bazan, J.F. / Yoshimi, A. / Savvides, S.N.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 25, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Leukocyte tyrosine kinase receptor
D: Nb3.16
B: Leukocyte tyrosine kinase receptor
E: Nb3.16
A: ALK and LTK ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6579
Polymers100,5655
Non-polymers924
Water12,214678
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-62 kcal/mol
Surface area35060 Å2
Unit cell
Length a, b, c (Å)129.110, 129.110, 109.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
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,z+1/2

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Components

#1: Protein Leukocyte tyrosine kinase receptor / Protein tyrosine kinase 1


Mass: 32069.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTK, TYK1 / Production host: Homo sapiens (human)
References: UniProt: P29376, receptor protein-tyrosine kinase
#2: Antibody Nb3.16


Mass: 13690.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Komagataella phaffii (fungus)
#3: Protein ALK and LTK ligand 1 / Augmentor beta / AUG-beta / Protein FAM150A


Mass: 9045.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKAL1, FAM150A, UNQ9433/PRO34745 / Production host: Homo sapiens (human) / References: UniProt: Q6UXT8
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: MOPSO/BIS-TRIS pH 6.5 20% PEG 8000 40% w/v 1,5-pentanediol 5mM Na2CrO4 . 4H2O 5mM Na2MoO4 . 4H2O 5mM Na2WO4 . 4H2O 5mM Na2VO4 . 4H2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→42.3 Å / Num. obs: 75541 / % possible obs: 99.9 % / Redundancy: 20.8 % / Biso Wilson estimate: 38.41 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.076 / Net I/σ(I): 26.6
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 5362 / CC1/2: 0.88 / Rrim(I) all: 1.47

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NX1
Resolution: 1.95→42.26 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 3778 5 %
Rwork0.1689 71763 -
obs0.1703 75541 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.43 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 4 678 7184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556648
X-RAY DIFFRACTIONf_angle_d0.89898980
X-RAY DIFFRACTIONf_chiral_restr0.0474906
X-RAY DIFFRACTIONf_plane_restr0.00541210
X-RAY DIFFRACTIONf_dihedral_angle_d14.74552312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.25131280.24322445X-RAY DIFFRACTION92.39
1.97-20.2361400.23522649X-RAY DIFFRACTION99.93
2-2.030.26261400.22722653X-RAY DIFFRACTION99.96
2.03-2.060.25231390.22442643X-RAY DIFFRACTION99.86
2.06-2.090.26071400.22012666X-RAY DIFFRACTION99.93
2.09-2.120.25351420.20492690X-RAY DIFFRACTION99.96
2.12-2.150.2131380.19222633X-RAY DIFFRACTION100
2.15-2.190.22241410.18982668X-RAY DIFFRACTION99.96
2.19-2.230.21741390.18762649X-RAY DIFFRACTION100
2.23-2.270.23371390.18692641X-RAY DIFFRACTION100
2.27-2.320.22731410.18932669X-RAY DIFFRACTION99.96
2.32-2.370.21551390.18772649X-RAY DIFFRACTION100
2.37-2.420.22991410.18052677X-RAY DIFFRACTION100
2.43-2.490.2411400.17532661X-RAY DIFFRACTION100
2.49-2.550.23311390.17582636X-RAY DIFFRACTION99.96
2.55-2.630.21661410.17792677X-RAY DIFFRACTION100
2.63-2.710.22311390.18212645X-RAY DIFFRACTION99.96
2.71-2.810.24991420.1822700X-RAY DIFFRACTION100
2.81-2.920.21561410.17982669X-RAY DIFFRACTION100
2.92-3.050.21131380.16812633X-RAY DIFFRACTION100
3.06-3.220.16451410.17042680X-RAY DIFFRACTION100
3.22-3.420.21671410.16672676X-RAY DIFFRACTION100
3.42-3.680.20761410.16612681X-RAY DIFFRACTION100
3.68-4.050.14261410.14842675X-RAY DIFFRACTION100
4.05-4.640.16781410.12522674X-RAY DIFFRACTION100
4.64-5.840.15691420.14592694X-RAY DIFFRACTION100
5.84-42.260.18411440.18852730X-RAY DIFFRACTION99.83
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.47463703457-0.704436133575-0.1955411270485.771389390040.4902963686622.63275344382-0.0623518662687-0.09654953166010.1893112151440.2257286754220.174155192180.0184790665122-0.3080677309220.00428203298873-0.115978442250.265663566212-0.00359996726172-0.003076903536890.201804843422-0.008404691598920.233944599713-45.203744428924.62964412888.91445763048
29.35758208806-1.870033053112.571591585862.05040821123-0.8705991724132.4614968114-0.092066838526-0.431913505514-0.01985009177540.0487450316540.0346165344093-0.129124747226-0.01936293740310.0174016585440.04502657194040.3250473020080.05289454041370.04095083643230.241666979629-0.04686798486960.157646453359-46.237466153414.67411025239.81765491782
36.59982617256-1.946741890751.243661278271.98969186563-0.1930858074561.55958688528-0.198246276506-0.330719758905-0.2592594418130.03705996028840.1332010920040.167450704352-0.0311056777651-0.01874755622040.02415325164910.3524189438170.01073030505730.009086889649760.259623112109-0.003491143840430.218838998001-51.377400422913.52214229167.60842575444
41.71873813648-1.95769008752-1.151117544649.018435444462.773512318059.52244096731-0.0984566771021-0.160091744622-0.5242674528860.337902951432-0.05232913749820.8703530795090.0519090631112-1.246350134950.175109575070.3911107447890.125649641437-0.08325043066990.6634698467470.01541994287870.562506299119-79.044034810318.966718243-5.1780675906
55.88695043786-0.2515777432950.8283127635481.88030048578-0.139333828521.035282864-0.07252850262650.15435999535-0.267277122892-0.236537754186-0.00105477951717-0.05357547221250.008611847420990.06240407229470.02219928846810.3948428639850.01682836345090.02119387300090.252240326934-0.01800161808790.256525605414-48.658109031711.9575924178-1.40447857753
62.71006438682-0.9448195642270.9420331803291.60561823999-0.04698979290812.46722129715-0.190886263042-0.355188194525-0.896754331680.2582287677930.1799937065370.6971059243510.214048054964-0.416938386421-0.1107167477480.395700784131-0.06070507882330.02742416361150.3405989788430.06151108977970.541054939194-63.23775245753.502092589581.972656197
73.11538977235-3.201279737992.061825314113.57875956376-1.565704076712.513261332570.4401562026080.0889537031519-0.778697206902-0.408306230878-0.1807552305210.2437956107610.3556167913210.149855707743-0.09988649079850.4696474131290.0230698148311-0.01797476266940.375067086114-0.01426353524010.397445347986-48.78310987965.12308930194-6.5543221
82.97750605857-1.992087683952.839514069113.2371340357-0.8860633936153.17320420627-0.06061278731450.5389030941460.262305103262-0.323164326163-0.1023570737690.0781210798935-0.05166166607230.1077952174550.1369332129450.4418974340550.0151008029867-0.0320314565450.4098830942610.02117263294180.333754034186-51.496725746515.5839938527-9.28438104346
97.02076302915-3.579308285632.507610506692.38025477253-1.357419019331.705165661320.1453316531940.243567432853-0.448129778357-0.193601143262-0.1141750298250.2920388601270.147610899838-0.062292995697-0.04553607919210.3729165934330.00154320997897-0.02115372169640.304200853487-0.02352512893650.315496438722-58.996123929110.2700599455-4.29299338232
103.91258656561-0.3895420296212.796597071685.87868222037-2.888391636314.97912049217-0.324688043233-0.556096462475-0.2956292179270.5412571255740.2126042155670.3008543749830.1705040469240.08528864422430.1203501296280.4054821624010.06190668430120.09374563533270.39801368978-0.002454453002870.258696949657-47.6081209238.0833039693715.4072755984
119.183440112780.3706479463297.703842957213.3103233019-0.4298475624117.528723925690.1830280458270.0680027175665-0.560630071366-0.743819146496-0.167397054488-0.2780630523160.708215089696-0.2735305370310.01975627116620.604478240944-0.04280929493060.1774880628640.435302763419-0.03213137395210.415160908-16.13076257314.3307826542-18.4624482416
125.06003519379-3.54368590527-1.131276410029.75203410368-3.351686756456.652755650160.05196893039050.00290344127851-0.982332271246-0.4256853734510.1084497259960.5819445917650.571339082879-0.144219939708-0.2120837308330.367881025548-0.07342538623860.04176061014890.3103843625280.04125460915060.429844849643-25.035773435614.0435965272-10.1141448413
133.434974158280.318928839-1.189326673992.932743276920.1730273413980.743960122636-0.07833139318570.00115454371505-0.0366636602606-0.2589173353110.0517736159068-0.1061961189650.08785345725670.04308422456810.04374537792110.431209407894-0.0254235369550.04230775265810.338978001590.01368054753480.325446326208-22.131388955621.3384925558-10.4814249223
149.26168543023-0.750655584828-4.702076900583.262989398650.4987281965094.61708527005-0.524599243130.193554520461-0.806370435043-0.2591328495890.0539603539380.02716541910570.577430427374-0.1060390006710.4456655087920.509176839712-0.03843774407960.1007156272760.2488893222760.02116718307360.413033744887-23.484495940510.2922735131-11.943587694
152.537746659330.000238650783479-0.4558106543571.19725233786-0.1261709606441.81844663189-0.0392172925074-0.1587664641230.0261601456520.0676205302926-0.03074898344320.308951864064-0.0051835188754-0.2475269516530.0530289404330.3765191369660.05754723931610.01750039631140.360686209081-0.04187002849460.434804442165-74.220305612919.198425765516.2047737295
164.294176012161.23872487305-0.5851481551861.53310794636-0.7558397356291.70601967950.0421831959857-0.2421527513960.1479572455250.3163267596230.007953111552880.229055798304-0.234806624172-0.232408411548-0.1203010731390.4923478381390.0868521284450.08582445183220.376127207591-0.09526055383610.460429388173-70.557703270127.155002587226.2870960862
173.414095542421.01712601652-0.09167927626943.84247379814-1.20258075381.511263587910.148806393933-0.7643257848580.8196740866180.461168690996-0.1393894043850.306866083323-0.0603927804837-0.181632571549-0.1105909049650.5045825342960.0600887099290.1265163257660.458932316992-0.1394824733820.651476758295-78.393596669633.623419596124.3935248989
182.387553633890.550547259136-0.453138252791.98016238297-0.5215979879161.90905794392-0.0612369082006-0.2799382657830.1950698683810.2199769004390.0354326702240.165043746317-0.0603307545087-0.1096412146090.01024053973130.3941468932920.05453096294590.04647636903790.397999215869-0.06975786760690.439178199914-70.521949038625.519123418622.9019182161
191.51038255227-0.1805851658631.34689494593.181511744021.638957933812.23338229142-0.912949444267-0.295424608349-0.9123250799520.5456960478780.4082799529850.686215217649-0.0223286024461-1.097462505480.2472750550190.6681959931350.1674623353620.2073661367681.304727177930.1150484781990.925238461636-112.21791979527.689637320437.1859669507
204.1766338553-2.53477697681-0.3814364311547.129016988480.0915488906924.43548901891-0.0962463377735-0.9042828049570.7356151735260.1949043729090.4574832320990.190770553569-0.583418005537-0.556887338712-0.3198930836850.5571799440940.1659000460460.07756870883271.01327066567-0.1165935851760.675013537248-105.360912929.516595972828.1774989557
213.69564064132-2.228856378350.1739450252046.17615364578-1.051032561585.9565228571-0.580950722171-1.25083031617-0.1674627303260.8911572066530.6550983196010.151312123107-0.0889810450524-0.353270147-0.2262103448120.5371054715160.1679146188780.09349018472150.9977147636380.05756394791790.559439453417-103.13888823418.799546826732.8255390783
223.58192929511-2.108142481760.3116330757564.263598774691.773829481065.71916254861-0.147472877551-0.6997492643550.005271435264470.2509197585810.1628339994640.5293231358770.0974264550867-0.948621045850.03490493123670.3883418141130.02867215210810.06691157963840.823224154863-0.06099818398790.637881533546-108.5929975622.680820975426.5513402192
235.05381458002-1.38102845672-0.7485026676094.897249234632.308329520126.00184226055-0.307004304437-1.315969870120.09853061123851.04141050620.625389677705-0.380014345944-0.0877838687497-0.0346959461224-0.2637041157260.5470288077450.18745316780.02114470024310.928213185602-0.003506011552780.638622645865-100.46071768926.471362586533.9642324737
244.8835775924-1.57063867709-4.499148216841.505572693553.095809802326.83892677315-0.547158578975-0.920841004188-0.9113433707361.291379097180.4063110449060.02446829646190.9071226108010.2278767922290.2844170887190.8197740475450.144997212570.1565766773480.7104550163030.1648829330040.508343371491-52.06841555633.8341717058426.8472877218
255.43144338015-1.21996137516-1.237485184255.185149894580.9376756932942.04241451933-0.694763877056-0.952320140196-0.5986403982070.9995886291950.04336804706730.8888782192970.809215362682-0.4597982072690.4970829722840.8791042861510.133727823560.3222651413430.6603819564850.1825147449680.846043952034-63.4360472743.020500687731.6016110655
265.558539992650.464054152447-0.3765935470969.202843141686.734790268624.97886102255-0.416395533377-0.308635536528-0.309334443910.1349413199830.4731418894220.1047331343250.0994655345610.4466359934910.159060014070.5153892672750.02022827304490.06685949591470.6132812322060.07981495286120.617921884932-59.74452970979.0326544382624.0764940309
274.00677518724.84412055629-4.957633934865.86331775119-6.016315103776.16924497990.279490480580.809376286624-0.0734609660649-0.2771296535830.0207185978556-0.4581782458880.383497071559-0.579896035241-0.3944086132821.085219114640.03255405694160.1680190840250.9064775745640.06336599838640.584640629871-58.505655883613.762103296740.365470166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 66 through 105 )
2X-RAY DIFFRACTION2chain 'C' and (resid 106 through 134 )
3X-RAY DIFFRACTION3chain 'C' and (resid 135 through 172 )
4X-RAY DIFFRACTION4chain 'C' and (resid 173 through 189 )
5X-RAY DIFFRACTION5chain 'C' and (resid 190 through 231 )
6X-RAY DIFFRACTION6chain 'C' and (resid 232 through 257 )
7X-RAY DIFFRACTION7chain 'C' and (resid 258 through 277 )
8X-RAY DIFFRACTION8chain 'C' and (resid 278 through 300 )
9X-RAY DIFFRACTION9chain 'C' and (resid 301 through 357 )
10X-RAY DIFFRACTION10chain 'C' and (resid 358 through 379 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 23 )
12X-RAY DIFFRACTION12chain 'D' and (resid 24 through 45 )
13X-RAY DIFFRACTION13chain 'D' and (resid 46 through 109 )
14X-RAY DIFFRACTION14chain 'D' and (resid 110 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 66 through 189 )
16X-RAY DIFFRACTION16chain 'B' and (resid 190 through 264 )
17X-RAY DIFFRACTION17chain 'B' and (resid 265 through 292 )
18X-RAY DIFFRACTION18chain 'B' and (resid 293 through 378 )
19X-RAY DIFFRACTION19chain 'E' and (resid 2 through 17 )
20X-RAY DIFFRACTION20chain 'E' and (resid 18 through 39 )
21X-RAY DIFFRACTION21chain 'E' and (resid 40 through 52 )
22X-RAY DIFFRACTION22chain 'E' and (resid 53 through 108 )
23X-RAY DIFFRACTION23chain 'E' and (resid 109 through 124 )
24X-RAY DIFFRACTION24chain 'A' and (resid 71 through 87 )
25X-RAY DIFFRACTION25chain 'A' and (resid 88 through 106 )
26X-RAY DIFFRACTION26chain 'A' and (resid 107 through 121 )
27X-RAY DIFFRACTION27chain 'A' and (resid 122 through 128 )

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