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- PDB-7xm4: Crystal structure of Keap1 Kelch domain (residues 322-609) in com... -

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Basic information

Entry
Database: PDB / ID: 7xm4
TitleCrystal structure of Keap1 Kelch domain (residues 322-609) in complex with 6e
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 / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / regulation of autophagy / 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 / Kelch motif / 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 / 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
Chem-GDJ / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Oct 16, 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)32,6892
Polymers31,9371
Non-polymers7521
Water00
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 area11500 Å2
Unit cell
Length a, b, c (Å)126.762, 76.277, 48.106
Angle α, β, γ (deg.)90.000, 105.240, 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-GDJ / N-[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]-2-(4-ethylpiperazin-1-yl)ethanamide


Mass: 751.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H41N7O8S2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.51 Å3/Da / Density % sol: 64.99 %
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: 2.7→50 Å / Num. obs: 12192 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.08 Å2 / Rmerge(I) obs: 0.228 / Net I/σ(I): 11.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 1.159 / Num. unique obs: 1210

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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: 2.7→42.78 Å / SU ML: 0.3174 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.2539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 2356 9.96 %
Rwork0.177 21304 -
obs0.183 12191 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.64 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 0 0 2213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752324
X-RAY DIFFRACTIONf_angle_d0.99133172
X-RAY DIFFRACTIONf_chiral_restr0.0527322
X-RAY DIFFRACTIONf_plane_restr0.0053414
X-RAY DIFFRACTIONf_dihedral_angle_d11.8693340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.30581350.27441258X-RAY DIFFRACTION97.69
2.76-2.820.34041390.23781239X-RAY DIFFRACTION99.28
2.82-2.880.26051400.21011230X-RAY DIFFRACTION99.28
2.88-2.950.28111400.221270X-RAY DIFFRACTION99.3
2.95-3.030.27251430.19821272X-RAY DIFFRACTION99.51
3.03-3.120.28311410.20871238X-RAY DIFFRACTION99.49
3.12-3.220.22321400.18211275X-RAY DIFFRACTION99.23
3.22-3.340.27871370.18391255X-RAY DIFFRACTION99.57
3.34-3.470.21541360.17171242X-RAY DIFFRACTION99.21
3.47-3.630.2561350.16631247X-RAY DIFFRACTION99.71
3.63-3.820.1991440.15991268X-RAY DIFFRACTION99.65
3.82-4.060.21371320.16021260X-RAY DIFFRACTION99.43
4.06-4.370.19831440.13741259X-RAY DIFFRACTION99.22
4.38-4.810.18641350.14011246X-RAY DIFFRACTION99.42
4.82-5.510.22131430.16191241X-RAY DIFFRACTION99.35
5.51-6.930.2541390.19911271X-RAY DIFFRACTION99.16
6.95-42.780.26461330.19471233X-RAY DIFFRACTION97.78

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