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- PDB-7xm5: Keap1 Kelch domain (residues 322-609) in complex with 6i -

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Basic information

Entry
Database: PDB / ID: 7xm5
TitleKeap1 Kelch domain (residues 322-609) in complex with 6i
ComponentsKelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / oxidative stress sensor
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 / disordered domain specific binding / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / regulation of autophagy / protein ubiquitination / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytoplasm / cytosol
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
Chem-GCI / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, K.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Crystallography-Guided Optimizations of the Keap1-Nrf2 Inhibitors on the Solvent Exposed Region: From Symmetric to Asymmetric Naphthalenesulfonamides.
Authors: Liu, G. / Hou, R. / Xu, L. / Zhang, X. / Yan, J. / Xing, C. / Xu, K. / Zhuang, C.
History
DepositionApr 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6752
Polymers31,9371
Non-polymers7391
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11320 Å2
Unit cell
Length a, b, c (Å)126.247, 76.211, 48.203
Angle α, β, γ (deg.)90.000, 105.212, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 31936.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical ChemComp-GCI / N-[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]-3-morpholin-4-yl-propanamide


Mass: 738.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38N6O9S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17393 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.04 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 1.176 / Num. unique obs: 1683

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XMB

4xmb


Resolution: 2.4→40.52 Å / SU ML: 0.2771 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 3368 9.98 %
Rwork0.1736 30389 -
obs0.178 17389 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 51 57 2272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722325
X-RAY DIFFRACTIONf_angle_d0.98523173
X-RAY DIFFRACTIONf_chiral_restr0.0579324
X-RAY DIFFRACTIONf_plane_restr0.0049412
X-RAY DIFFRACTIONf_dihedral_angle_d21.367351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.35711330.30091222X-RAY DIFFRACTION95.56
2.43-2.460.3251410.26051260X-RAY DIFFRACTION98.38
2.46-2.50.30161420.2461273X-RAY DIFFRACTION99.72
2.5-2.540.25821440.23141300X-RAY DIFFRACTION98.5
2.54-2.590.2951340.23641200X-RAY DIFFRACTION99.55
2.59-2.630.32161470.21941335X-RAY DIFFRACTION98.87
2.64-2.690.24761370.21491251X-RAY DIFFRACTION99.64
2.69-2.740.22981380.20471257X-RAY DIFFRACTION98.87
2.74-2.80.2531430.1881287X-RAY DIFFRACTION99.58
2.8-2.870.23481400.17041248X-RAY DIFFRACTION99.21
2.87-2.940.25111410.16741289X-RAY DIFFRACTION99.17
2.94-3.020.20231440.17791292X-RAY DIFFRACTION99.45
3.02-3.10.20351420.18011249X-RAY DIFFRACTION99.29
3.11-3.20.21731430.16581296X-RAY DIFFRACTION99.58
3.21-3.320.21781400.16951256X-RAY DIFFRACTION99.22
3.32-3.450.24471390.15441278X-RAY DIFFRACTION99.44
3.45-3.610.19061460.16471282X-RAY DIFFRACTION99.58
3.61-3.80.20081360.16031253X-RAY DIFFRACTION99.29
3.8-4.040.19881410.15491270X-RAY DIFFRACTION99.23
4.04-4.350.19181470.13341285X-RAY DIFFRACTION99.1
4.35-4.790.18371400.1351248X-RAY DIFFRACTION98.44
4.79-5.480.16481380.15661255X-RAY DIFFRACTION98.65
5.48-6.90.24121370.1911287X-RAY DIFFRACTION98.07
6.9-40.520.20161350.18811216X-RAY DIFFRACTION95.61

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