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- PDB-9etw: BTB domain of KLHL26 -

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Basic information

Entry
Database: PDB / ID: 9etw
TitleBTB domain of KLHL26
ComponentsKelch-like protein 26
KeywordsLIGASE / BTB / KLHL26 / KEAP1
Function / homology
Function and homology information


Kelch-like protein 26 / Kelch motif / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller ...Kelch-like protein 26 / Kelch motif / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Kelch-like protein 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsRichardson, W. / Bullock, A.N. / Rothweiler, E.M. / Manning, C.E. / Sweeney, M.N. / Chalk, R. / Huber, K.V.M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: J.Med.Chem. / Year: 2024
Title: Covalent Inhibitors of KEAP1 with Exquisite Selectivity.
Authors: Fejes, I. / Markacz, P. / Tatai, J. / Rudas, M. / Dunkel, P. / Gyuris, M. / Nyerges, M. / Provost, N. / Duvivier, V. / Delerive, P. / Martiny, V. / Bristiel, A. / Vidal, B. / Richardson, W. ...Authors: Fejes, I. / Markacz, P. / Tatai, J. / Rudas, M. / Dunkel, P. / Gyuris, M. / Nyerges, M. / Provost, N. / Duvivier, V. / Delerive, P. / Martiny, V. / Bristiel, A. / Vidal, B. / Richardson, W. / Rothweiler, E.M. / Tranberg-Jensen, J. / Manning, C.E. / Sweeney, M.N. / Chalk, R. / Huber, K.V.M. / Bullock, A.N. / Herner, A. / Seedorf, K. / Vinson, C. / Weber, C. / Kotschy, A.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 26
B: Kelch-like protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1073
Polymers28,0452
Non-polymers621
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-34 kcal/mol
Surface area11880 Å2
Unit cell
Length a, b, c (Å)28.740, 78.186, 95.571
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

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Components

#1: Protein Kelch-like protein 26


Mass: 14022.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL26 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: Q53HC5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.91 Å3/Da / Density % sol: 35.75 % / Description: Prismatic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.2M sodium acetate & 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.51→40.77 Å / Num. obs: 34811 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.055 / Net I/σ(I): 7.3
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 1678 / CC1/2: 0.361 / Rpim(I) all: 0.857 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→39.09 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2182 1783 5.15 %
Rwork0.188 32815 -
obs0.1896 34598 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.34 Å2
Refinement stepCycle: LAST / Resolution: 1.51→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 4 164 2044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961974
X-RAY DIFFRACTIONf_angle_d12686
X-RAY DIFFRACTIONf_chiral_restr0.0581327
X-RAY DIFFRACTIONf_plane_restr0.0099344
X-RAY DIFFRACTIONf_dihedral_angle_d11.515721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.38631240.3892317X-RAY DIFFRACTION94.65
1.55-1.60.3551120.34682548X-RAY DIFFRACTION99.96
1.6-1.650.33321150.30392481X-RAY DIFFRACTION100
1.65-1.710.3241500.26522495X-RAY DIFFRACTION99.92
1.71-1.780.281320.23812504X-RAY DIFFRACTION100
1.78-1.860.28251540.22652484X-RAY DIFFRACTION99.96
1.86-1.950.24841390.22652524X-RAY DIFFRACTION99.96
1.95-2.080.24041430.18232521X-RAY DIFFRACTION99.96
2.08-2.240.20681600.1692501X-RAY DIFFRACTION99.96
2.24-2.460.22561250.16852545X-RAY DIFFRACTION100
2.46-2.820.20631350.17322566X-RAY DIFFRACTION100
2.82-3.550.1821390.16212601X-RAY DIFFRACTION100
3.55-39.090.17591550.15792728X-RAY DIFFRACTION99.93
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)
16.1067403525-4.355145486927.581775159733.38872181157-5.066064978319.242731564690.5901543794840.273397638653-0.7864370541260.1569000787430.0343640233259-0.3098276762161.093309096740.472354616751-0.5096793061880.3972366697050.0937048168645-0.0608393170380.225554839781-0.08768618564890.30150054152217.0613483045-13.2941457392-1.7773937584
24.55186600828-3.527790421991.085736717395.11771443727-0.759264393271.54106904778-0.0947287349084-0.104763257811-0.1730857867940.1414352944160.07248012001630.2336682483690.0629535230573-0.1500850424840.01414314232770.1462102821-0.0222290215912-0.006795841029230.192988447375-0.005034581055390.127953326508-1.564824186541.24957052066-7.82484626446
36.254098237130.2960604773035.265788270915.57603308653-0.05188634523538.73547120457-0.333517495183-0.1719030781790.263504284842-0.3107020341860.1659938302350.37302043675-0.557363226045-0.5160019074040.141399900370.1440642253650.0304367830703-0.002871229390660.177870719925-0.01819962461130.170470647226-7.277176210312.0071379421-21.1109247107
46.31472781158-1.29190427697-0.4572683147483.972062836020.2148464377464.90034666878-0.03584937232960.122893102180.192648388207-0.1218563640130.0790462159555-0.187369784872-0.02739420898380.247651485304-0.04331388861240.0959730967298-0.00259364285617-0.008020465080560.131908771002-0.0131513085050.1326296767066.274626780416.23312746586-21.290493728
55.61957702311-2.396270228030.4827584674251.60861541563-0.3586784317363.05541517475-0.05573556922920.6239598548151.010244646-0.886840737036-0.185283033655-0.58185321173-0.624249658124-0.186310723082-0.05462954915340.372071201562-0.03075005488180.02698679452880.3177909579330.02399771053640.4678390010877.0823438289217.3959174021-24.5393820338
62.645219291067.821551057453.931916296012.720757484875.284132003268.67930712479-0.3390097479950.2792803497020.332558329682-0.4747978556760.2962445885660.114679367759-0.9022683120320.3581217622690.2087019428290.282363073795-0.00921219829114-0.0297418047530.194557099703-0.021156859930.267587585374-3.0143247403914.2956971632-25.9785086766
72.46227657618-1.260308963314.265907090671.77852055825-2.569628442097.60767638591-0.00460732050713-0.129750826445-0.0601208410149-0.0312000628140.08988563255780.1847539073340.145229068432-0.374830244-0.1432641382320.1468157933920.0018532899260.006479569202920.168375462983-0.01416808519030.188452918812-7.009843212090.857902523948-21.3127761802
89.43851499320.9657173998257.928102867595.01616454020.4917053847722.207530559050.112132650093-0.393862068096-0.2710621312820.2279792582030.02833237949040.1254709304760.173403045179-0.56123226073-0.3743116367760.190902712791-0.0231657377380.01255847618480.186366045851-0.008100288603440.141407213737-11.9536984753-6.84975967361-25.1772228135
99.435004604522.22383267224-2.689787581835.0551619532-2.700229773273.99798519095-0.2043777991940.238599159083-0.14915520921-0.2122993074160.09437901073380.0855866652204-0.0573249690353-0.05163216047240.1223335821670.1678319456520.00412230187887-0.001580760031040.110040754593-0.02743736461780.126310831252-3.42512211809-0.23823346235-30.2033216932
109.120105288868.633787436542.815138079518.925287946813.595652030095.371953207140.1229308970750.155485089683-0.637438436151-0.1497815918840.0377838895363-0.3463022793720.428440106035-0.0313692043069-0.1356515785040.206214965079-0.00424848070403-0.01040201490830.137029458250.005546438715770.205806792713-5.49419949816-11.3518132991-30.8516353368
112.024695192681.252586116212.046559846586.673695953820.0003290443570586.776031240970.727591553181-0.185647442872-1.24136402139-0.211418063008-0.03526183402010.3179736905930.715728828842-0.625159528953-0.7390277176820.303164141852-0.0479715377883-0.03022659592840.2219527990340.0004426822111790.240625414206-7.24038796561-12.2007308627-21.7053211012
129.526992086497.921213396963.089604228028.689233864141.226920330652.23542567420.000843337505410.0571383728379-0.377475115403-0.09233226492620.0378338325069-0.4259734777770.2076814864460.336661458611-0.04623162296610.138573531310.03522493726550.01449228900050.175411422016-0.02482649452880.15856947239110.3520412633-1.87103219431-14.2113057562
131.79785993442-1.01038780425-2.921782973824.760106647320.2338209959982.166249559870.0816768738228-0.07843358886080.08279664427410.2345180222640.0905857367469-0.0793027963778-0.5113724767760.0468361752221-0.1529521888760.0941876608425-0.0143461035718-0.00365531202260.159743975550.006702060974740.14049016525514.398998490811.1069605622-4.87224746403
144.931451534451.72654778287-0.9781495982282.79753765006-0.2601386789814.562316097010.0114665418648-0.0473904954020.0281458583820.1671942442860.0279280420782-0.01466225625810.1269843682850.113197709799-0.02315486582840.1234703384630.00887613564775-0.006497635148150.114582672597-0.002831066745390.1134319450279.801619338085.78090648906-3.06523880501
156.71408729284-2.59065994641-1.883773906168.79832344239-2.108459695982.31930164368-0.145952810152-0.2056326534540.1125288567030.4510845653980.1653247065940.229999897298-0.122953951525-0.541864776855-0.08248414741490.1549970231720.00416197312840.004271262360210.2318311892660.003008033592680.1211692664961.649932095825.970463291042.22761879962
162.032173986427.02123418804-8.908826808198.68555372876-6.343970959412.040796250771.44324914017-0.3828186282232.291819949420.808089343862-0.1017939099061.49368820357-0.945378460569-1.31329570642-1.220917144750.4802978995120.03168822113910.0214934148760.6138642498440.05067996028030.5874399925194.3781789397516.57993894781.46230860554
176.32729969495-6.198444024336.113590943568.19177776866-4.46169950947.02375381234-0.15656563893-0.3324454674930.1885949052020.681325712981-0.0174129604393-0.0897461275662-0.623986744682-0.1105215074010.08314856718930.15947858263-0.0276684451320.02501711580870.220344970409-0.009751164757920.1877742613413.009235266810.45141323827.23595108104
188.581948533115.025772940299.000944979976.974095399256.841958899312.44931782450.1133378704960.496838205084-0.183798699910.004883793325060.108524466054-0.3429773700570.3622050584420.844896437452-0.2618750671470.1744461461690.00702571560930.008011240361790.229673987820.03731430424490.1558806472616.7449527903-0.3151530436740.891768175967
199.76478439179-6.928060128656.614363031118.84740754446-7.025097373732.57986200413-0.185248363485-0.227180679001-0.1620131731750.3847726024910.134289671674-0.309140804068-0.2462107054840.333763010350.06978416309160.2630583548180.0865321654194-0.01044084064370.264443621972-0.03710045327730.1412418832519.2663157988-6.984731312410.460883531819
202.17741471572-0.4819137186432.826360774682.982967193710.6366363893944.704341206650.09560337864320.228239577684-0.120691905395-0.122901279683-0.05048644823430.01744827800220.2492021138980.0254759217924-0.08107200946060.213518696940.003943291745310.0111411954160.1607217281750.0174433854540.15065104550312.4882057462-2.730578234878.62115502785
219.71898221663-8.695769866051.349276508152.57174442252-1.664767834712.479437611880.382737854639-0.121716698598-1.90758902189-0.1216960942770.1951879628730.8612181239371.10866060733-0.088902983615-0.4073612970250.4918081758970.00356051370221-0.1102576824640.239502511439-0.009133691311990.40352311111214.2416210896-13.844232536.57652388787
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 45 )AA37 - 451 - 9
22chain 'A' and (resid 46 through 65 )AA46 - 6510 - 29
33chain 'A' and (resid 66 through 78 )AA66 - 7830 - 42
44chain 'A' and (resid 79 through 94 )AA79 - 9443 - 58
55chain 'A' and (resid 95 through 101 )AA95 - 10159 - 65
66chain 'A' and (resid 102 through 111 )AA102 - 11166 - 75
77chain 'A' and (resid 112 through 124 )AA112 - 12476 - 88
88chain 'A' and (resid 125 through 133 )AA125 - 13389 - 97
99chain 'A' and (resid 134 through 146 )AA134 - 14698 - 110
1010chain 'A' and (resid 147 through 161 )AA147 - 161111 - 125
1111chain 'B' and (resid 37 through 45 )BB37 - 451 - 9
1212chain 'B' and (resid 46 through 59 )BB46 - 5910 - 23
1313chain 'B' and (resid 60 through 72 )BB60 - 7224 - 36
1414chain 'B' and (resid 73 through 86 )BB73 - 8637 - 50
1515chain 'B' and (resid 87 through 94 )BB87 - 9451 - 58
1616chain 'B' and (resid 95 through 103 )BB95 - 10359 - 67
1717chain 'B' and (resid 104 through 111 )BB104 - 11168 - 75
1818chain 'B' and (resid 112 through 122 )BB112 - 12276 - 86
1919chain 'B' and (resid 123 through 133 )BB123 - 13387 - 97
2020chain 'B' and (resid 134 through 146 )BB134 - 14698 - 110
2121chain 'B' and (resid 147 through 161 )BB147 - 161111 - 125

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