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- PDB-9kvw: Crystal Structures of Keap1-compound complexes -

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Basic information

Entry
Database: PDB / ID: 9kvw
TitleCrystal Structures of Keap1-compound complexes
ComponentsKelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / complex / inhibitor
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite / regulation of autophagy / disordered domain specific binding / KEAP1-NFE2L2 pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / protein ubiquitination / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 ...Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / 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 ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsZhuang, C.L. / Yu, R.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82022065 China
Ministry of Science and Technology (MoST, China)2021YFA1302200 China
CitationJournal: To Be Published
Title: Crystal structure of Keap1-CD10
Authors: Zhuang, C.L. / Yu, R.Z.
History
DepositionDec 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3762
Polymers31,5831
Non-polymers7931
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.584, 72.958, 48.057
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31583.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical ChemComp-A1EHH / ~{N}-[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]-3-(2-oxa-8-azaspiro[4.5]decan-8-yl)propanamide


Mass: 792.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H44N6O9S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350,0.1M potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 46608 / % possible obs: 98.5 % / Redundancy: 5.8 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.079 / Rrim(I) all: 0.177 / Χ2: 2.965 / Net I/σ(I): 5.2 / Num. measured all: 272286
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.44-1.495.30.54645070.7990.9420.2560.6051.06595.6
1.49-1.556.40.48646250.8860.9690.2030.5281.41697.4
1.55-1.626.60.43745920.8680.9640.1820.4741.70198.1
1.62-1.716.50.37946390.9120.9770.1620.4132.15298.5
1.71-1.816.50.3346520.9330.9820.1420.362.69798.7
1.81-1.956.10.27246590.9540.9880.1230.2993.43298.8
1.95-2.155.70.21747190.9680.9920.1030.2414.02799.1
2.15-2.465.50.18346920.9730.9930.0890.2044.36199.6
2.46-3.15.20.15147250.9790.9950.0760.1694.78699.6
3.1-504.50.11247980.9860.9960.0620.1295.03499.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ifj

4ifj


Resolution: 1.44→39.65 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2334 5.02 %
Rwork0.2162 --
obs0.217 46534 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 55 289 2486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d14.286339
X-RAY DIFFRACTIONf_chiral_restr0.11322
X-RAY DIFFRACTIONf_plane_restr0.022402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.470.29751530.24632455X-RAY DIFFRACTION94
1.47-1.50.28511360.22962572X-RAY DIFFRACTION97
1.5-1.540.28251290.22272566X-RAY DIFFRACTION97
1.54-1.570.25581410.21122513X-RAY DIFFRACTION98
1.57-1.620.25921310.21182623X-RAY DIFFRACTION98
1.62-1.670.21631260.20722603X-RAY DIFFRACTION99
1.67-1.720.22351520.20822577X-RAY DIFFRACTION98
1.72-1.780.30281320.21722607X-RAY DIFFRACTION98
1.78-1.850.25731420.21742592X-RAY DIFFRACTION98
1.85-1.940.24511390.22032609X-RAY DIFFRACTION99
1.94-2.040.22851180.21252637X-RAY DIFFRACTION99
2.04-2.170.27071330.21792605X-RAY DIFFRACTION99
2.17-2.330.21091340.22712629X-RAY DIFFRACTION99
2.33-2.570.24611370.22882655X-RAY DIFFRACTION100
2.57-2.940.22381490.2292634X-RAY DIFFRACTION100
2.94-3.70.21821420.21362642X-RAY DIFFRACTION99
3.7-39.650.21531400.20182681X-RAY DIFFRACTION99

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