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- PDB-8pqe: c-KIT kinase domain in complex with avapritinib derivative 11 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8pqe
Titlec-KIT kinase domain in complex with avapritinib derivative 11
ComponentsMast/stem cell growth factor receptor Kit
KeywordsTRANSFERASE / c-KIT protein kinase / avapritinib / inhibitor / tyrosine kinase / transmembrane receptor / stem cell factor / SCF / stem cell factor receptor / GIST / gastrointestinal stromal tumors / P10721
Function / homology
Function and homology information


Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants ...Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / Kit signaling pathway / positive regulation of small intestine smooth muscle contraction / regulation of bile acid metabolic process / positive regulation of dendritic cell cytokine production / positive regulation of mast cell proliferation / mast cell differentiation / mast cell chemotaxis / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of pseudopodium assembly / immature B cell differentiation / positive regulation of mast cell cytokine production / lymphoid progenitor cell differentiation / melanocyte differentiation / germ cell migration / erythropoietin-mediated signaling pathway / myeloid progenitor cell differentiation / digestive tract development / negative regulation of programmed cell death / lamellipodium assembly / embryonic hemopoiesis / tongue development / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of KIT signaling / megakaryocyte development / mast cell degranulation / pigmentation / stem cell population maintenance / positive regulation of Notch signaling pathway / growth factor binding / cytokine binding / spermatid development / negative regulation of reproductive process / negative regulation of developmental process / hemopoiesis / somatic stem cell population maintenance / T cell differentiation / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / response to cadmium ion / ovarian follicle development / transmembrane receptor protein tyrosine kinase activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Transcriptional and post-translational regulation of MITF-M expression and activity / B cell differentiation / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / acrosomal vesicle / erythrocyte differentiation / positive regulation of DNA-binding transcription factor activity / epithelial cell proliferation / cell chemotaxis / positive regulation of receptor signaling pathway via JAK-STAT / stem cell differentiation / placental growth factor receptor activity / Signaling by SCF-KIT / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / cytokine-mediated signaling pathway / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / visual learning / cytoplasmic side of plasma membrane / fibrillar center / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / cell migration
Similarity search - Function
Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-9WU / BROMIDE ION / Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTeuber, A. / Niggenaber, J. / Mueller, M.P. / Rauh, D.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Regional Development FundEFRE-800400European Union
German Federal Ministry for Education and Research01ZX2201B Germany
Other privateEx-2021-0033
Other governmentNW21-062C
CitationJournal: Nat Commun / Year: 2024
Title: Avapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA.
Authors: Teuber, A. / Schulz, T. / Fletcher, B.S. / Gontla, R. / Muhlenberg, T. / Zischinsky, M.L. / Niggenaber, J. / Weisner, J. / Kleinbolting, S.B. / Lategahn, J. / Sievers, S. / Muller, M.P. / Bauer, S. / Rauh, D.
History
DepositionJul 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Aug 7, 2024Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mast/stem cell growth factor receptor Kit
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6717
Polymers74,3892
Non-polymers1,2835
Water2,468137
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A: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8894
Polymers37,1941
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7823
Polymers37,1941
Non-polymers5882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.970, 62.520, 191.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 566 through 569 or (resid 570...
d_2ens_1(chain "B" and (resid 566 through 599 or (resid 600...
d_1ens_2chain "D"
d_2ens_2chain "E"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNLEULEUAA566 - 67919 - 132
d_12ens_1PHEPHEARGARGAA681 - 683134 - 136
d_13ens_1LYSLYSTYRTYRAA685 - 692138 - 145
d_14ens_1ASPASPPHEPHEAA762 - 772155 - 165
d_15ens_1TYRTYRCYSCYSAA774 - 788167 - 181
d_16ens_1HISHISGLYGLYAA790 - 866183 - 259
d_17ens_1SERSERALAALAAA868 - 897261 - 290
d_18ens_1METMETGLUGLUAA899 - 930292 - 323
d_21ens_1ASNASNILEILEBB566 - 61219 - 65
d_22ens_1SERSERLEULEUBB614 - 67967 - 132
d_23ens_1PHEPHEARGARGBB681 - 683134 - 136
d_24ens_1LYSLYSPHEPHEBB685 - 772138 - 165
d_25ens_1TYRTYRCYSCYSBB774 - 788167 - 181
d_26ens_1HISHISASPASPBB790 - 810183 - 203
d_27ens_1ARGARGGLYGLYBB830 - 866223 - 259
d_28ens_1SERSERALAALABB868 - 897261 - 290
d_29ens_1METMETGLUGLUBB899 - 930292 - 323
d_11ens_29WU9WU9WU9WUAD1002
d_21ens_29WU9WU9WU9WUBF1001

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.0294292295752, -0.997186737372, 0.0689386049728), (-0.999565953087, -0.0294523610378, 0.000681071191176), (0.00135124952405, -0.0689287257846, -0.997620671842)-2.19553305908, -15.8966439926, 47.1287137222
2given(0.00955481412757, -0.994359824302, 0.105627862525), (-0.999950267743, -0.00980321917973, -0.00183273950093), (0.00285789561595, -0.105605097928, -0.994404040481)-4.95391536619, -15.4489385782, 46.8542127835

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mast/stem cell growth factor receptor Kit / SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c- ...SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c-kit / v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog


Mass: 37194.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIT, SCFR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P10721, receptor protein-tyrosine kinase

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Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9WU / ~{N}-[(1~{S})-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethyl]prop-2-enamide


Mass: 552.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H29FN10O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 7.5 mg/mL, 12% PEG8000 20% Ethylen glycole, 30 mM NaI, 30 mM NaF, 30 mM NaBr, 100 mM Tris-Bicine, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 17, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→44.69 Å / Num. obs: 48848 / % possible obs: 100 % / Redundancy: 13.28 % / Biso Wilson estimate: 49.28 Å2 / CC1/2: 1 / Rrim(I) all: 0.067 / Net I/σ(I): 19.57
Reflection shellResolution: 2→2.1 Å / Redundancy: 13.98 % / Mean I/σ(I) obs: 1.22 / Num. unique obs: 6557 / CC1/2: 0.701 / Rrim(I) all: 2.25 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.69 Å / SU ML: 0.2714 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 2442 5 %
Rwork0.2135 46376 -
obs0.2156 48818 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.55 Å2
Refinement stepCycle: LAST / Resolution: 2→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 88 137 4573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394594
X-RAY DIFFRACTIONf_angle_d1.01476249
X-RAY DIFFRACTIONf_chiral_restr0.1571675
X-RAY DIFFRACTIONf_plane_restr0.0051787
X-RAY DIFFRACTIONf_dihedral_angle_d13.24481639
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.727274260396
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.53742237755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.43741420.41232698X-RAY DIFFRACTION99.89
2.04-2.090.40341420.38182680X-RAY DIFFRACTION99.82
2.09-2.130.41291400.352662X-RAY DIFFRACTION100
2.13-2.190.33931430.30632719X-RAY DIFFRACTION99.93
2.19-2.250.33461400.27962650X-RAY DIFFRACTION99.71
2.25-2.310.34991410.28122714X-RAY DIFFRACTION99.9
2.31-2.390.33481430.2482704X-RAY DIFFRACTION99.89
2.39-2.470.29581420.23462692X-RAY DIFFRACTION99.96
2.47-2.570.28181420.24472710X-RAY DIFFRACTION99.93
2.57-2.690.30021430.24652715X-RAY DIFFRACTION99.93
2.69-2.830.27861430.2552704X-RAY DIFFRACTION99.96
2.83-3.010.29581430.24192713X-RAY DIFFRACTION99.9
3.01-3.240.27241440.23382741X-RAY DIFFRACTION99.93
3.24-3.570.28061450.22382749X-RAY DIFFRACTION99.97
3.57-4.080.20651460.1862780X-RAY DIFFRACTION100
4.08-5.140.18691480.16192803X-RAY DIFFRACTION100
5.14-44.690.24271550.18722942X-RAY DIFFRACTION99.87
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)
15.873079679072.19601315485-1.611238781722.032310512860.004587895556592.55479701158-0.0467352055164-0.466500275152-0.3280336634120.116660998624-0.0375919117309-0.180970748054-0.07830476283220.1416811456910.05535168530350.4490624952870.0357885997024-0.02133638821090.5222473900230.001675818039680.480259025982-8.41433019088-2.0502891599462.2129447819
24.831443942681.896631323331.420199618133.2015363727-3.158280984316.18840353628-0.00742387245598-0.519507776816-0.00246471235078-0.0329463547923-0.2253670172490.365249924032-0.534332007268-0.9832470108810.3199042721610.589756671811-0.006923381149690.105733679710.636999995534-0.02052940754790.497008131481-24.0296155838-1.7954071796765.3542222245
36.668488966330.6299509637830.849459887062.07747090435-0.9811576936255.241977764210.0182814272757-1.40465228695-0.8448266465350.115818918905-0.4340985055140.1266199896720.3479823924920.1875551969170.2114050272120.569878145276-0.01623836493550.1712359535030.7102108448520.1823730703520.618455899245-16.6886267004-9.8323727246264.6549874968
43.301278199242.44602962984-1.400874003812.64752037013-0.2409045434842.66521724489-0.100814375847-0.22435498034-0.0456095494583-0.296939422249-0.677260332231-1.040492670920.423716506050.859715231477-0.232296924920.5579697033860.02612441285030.1344960072130.679632752112-0.01888544098660.701083687096-5.17942110339-6.0270119746259.5186628168
53.035725690430.3317078259661.375585699231.901019078070.2431174604997.7329549940.0298723879165-0.364380523353-0.2114041777690.07489336901180.153500356349-0.168637314102-0.627547245004-0.1293608545220.06006718158710.5173636414350.07384101202730.06667751123640.447134723239-0.01379230959190.550132180941-14.2452168565-1.2059563574259.1591350941
61.613106296580.3650654249851.762836719440.1640325641530.3269692223435.920494140230.07914792720470.00687820518906-0.0625214306318-0.0538520643264-0.1587426059140.2089728022890.406155554055-1.154990515240.07897949565340.496574146177-0.003602453708850.03375878474280.6886463080710.002792856570310.585492319184-29.2550056785-9.6898318633644.2860158743
73.644212392851.330424562652.246653790131.499312090270.9906112625665.293095609220.0807146582277-0.07786259802450.82409143651-0.0704192757576-0.2467392037910.0195775109256-0.477268120297-0.2681665270960.131507793610.5752189315270.04408101269170.02093910666420.4673906034790.02063271582170.557072803854-18.3679530487-1.8130664410838.9190390292
81.953197021920.9851183402050.5299494580431.834214711150.9347133292885.69685127920.0681969050697-0.437197989679-0.03396599427570.0770069644177-0.0058489875341-0.0826755076094-0.223719841762-0.13709517695-0.04272882928370.498821473265-0.009939653176360.02909069042840.543778942252-0.007209701450480.498547218419-16.4609725425-7.7523054492245.7897740911
92.61671757542-0.740542864029-0.3135270962694.638895629490.3636831094422.963466007240.06019494500970.0862718739407-0.123241880263-0.151766125615-0.00703513318606-0.142083616332-0.1135108064510.181746194859-0.05255032720990.350832276621-0.0240284865186-0.005511546795910.486840057209-0.01648266755050.406273964-12.0387713263-16.814325045933.1105338913
105.35202119535-1.052147175110.6886148258475.773261720280.02229869635254.936055211960.08411292397920.4582221268451.21020905152-0.464370511241-0.154661358267-0.13559954122-1.313878551090.214528559855-0.01356102207310.781386989048-0.01144897933080.06283839461250.4524850264230.0007729166864660.630551499093-16.11567393191.4361339920830.5917721375
111.93110112780.9514488459210.359200540242.92309013941-0.5975587645162.16281638773-0.150471476977-0.08545368361150.0164237980433-0.2710495556950.0715101883342-0.0689963593369-0.0673542378855-0.01064967543730.1031091453660.3183383471430.0526050166589-0.03106578887760.453637851077-0.01026861028560.3455562835655.77495106536-3.53085121957-14.4126175222
120.8951703749330.374652424714-1.522270550810.161000707849-0.6688983558582.686129450980.0290085439779-0.3852074898280.493293257993-0.0251902578724-0.03774733701550.349071717783-1.40163859128-0.06799187522250.1129092847140.8741501446290.0833876757965-0.08312587766480.593853221046-0.069484885620.6821736097319.8889810331813.41297874973.30993152996
133.63542008357-0.8193267739850.9941897817062.09789240051-0.7073589532333.64010128813-0.155378216439-0.3100129121070.1677287323450.09082425696340.04228279776430.0948032410868-0.335322657077-0.5724783469590.08244994070860.5060407685540.0703867074409-0.008600853763840.564751146619-0.06236797194840.40254350893411.3468931901-1.8197565203211.8519753723
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 566 through 600 )AA566 - 6001 - 35
22chain 'A' and (resid 601 through 616 )AA601 - 61636 - 50
33chain 'A' and (resid 617 through 630 )AA617 - 63051 - 64
44chain 'A' and (resid 631 through 647 )AA631 - 64765 - 81
55chain 'A' and (resid 648 through 666 )AA648 - 66682 - 100
66chain 'A' and (resid 667 through 765 )AA667 - 765101 - 131
77chain 'A' and (resid 766 through 786 )AA766 - 786132 - 152
88chain 'A' and (resid 787 through 808 )AA787 - 808153 - 174
99chain 'A' and (resid 809 through 916 )AA809 - 916175 - 263
1010chain 'A' and (resid 917 through 930 )AA917 - 930264 - 277
1111chain 'B' and (resid 566 through 666 )BC566 - 6661 - 101
1212chain 'B' and (resid 667 through 765 )BC667 - 765102 - 131
1313chain 'B' and (resid 766 through 930 )BC766 - 930132 - 283

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