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- PDB-7k2b: Kelch domain of human KEAP1 bound to Nrf2 peptide, ADEETGEFA -

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Basic information

Entry
Database: PDB / ID: 7k2b
TitleKelch domain of human KEAP1 bound to Nrf2 peptide, ADEETGEFA
Components
  • ACE-ALA-ASP-GLU-GLU-THR-GLY-GLU-PHE-ALA-NH2
  • Kelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING/Inhibitor / Peptide inhibitor / Inhibitor complex / Loop-mimic / PROTEIN BINDING / PROTEIN BINDING-Inhibitor complex
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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsMuellers, S.N. / Allen, K.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning.
Authors: Ortet, P.C. / Muellers, S.N. / Viarengo-Baker, L.A. / Streu, K. / Szymczyna, B.R. / Beeler, A.B. / Allen, K.N. / Whitty, A.
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
P: ACE-ALA-ASP-GLU-GLU-THR-GLY-GLU-PHE-ALA-NH2


Theoretical massNumber of molelcules
Total (without water)67,0363
Polymers67,0363
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)33,0221
Polymers33,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11800 Å2
MethodPISA
3
B: Kelch-like ECH-associated protein 1
P: ACE-ALA-ASP-GLU-GLU-THR-GLY-GLU-PHE-ALA-NH2


Theoretical massNumber of molelcules
Total (without water)34,0142
Polymers34,0142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint1 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.720, 68.755, 77.617
Angle α, β, γ (deg.)90.00, 117.60, 90.00
Int Tables number5
Space group name H-MC121
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: 33021.996 Da / Num. of mol.: 2 / Mutation: E540A, E542A
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: Protein/peptide ACE-ALA-ASP-GLU-GLU-THR-GLY-GLU-PHE-ALA-NH2


Mass: 991.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.5 M Ammonium Sulfate, 0.5-0.7% PEG-MME-550, 0.1 M Bis-Tris pH = 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.31→39.23 Å / Num. obs: 32606 / % possible obs: 97.99 % / Redundancy: 5.1 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.07009 / Rpim(I) all: 0.03323 / Rrim(I) all: 0.07792 / Net I/σ(I): 10.29
Reflection shellResolution: 2.311→2.393 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.98 / Num. unique obs: 3205 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.1742 / Rrim(I) all: 0.4107 / % possible all: 97.71

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFL

5wfl


Resolution: 2.31→39.23 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 1994 6.12 %
Rwork0.215 --
obs0.218 32601 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.18 Å2
Refinement stepCycle: LAST / Resolution: 2.31→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 0 175 4597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.31151480.23182152X-RAY DIFFRACTION98
2.37-2.430.26591360.23682159X-RAY DIFFRACTION98
2.43-2.50.25651400.24692148X-RAY DIFFRACTION97
2.5-2.580.28381480.25262179X-RAY DIFFRACTION98
2.58-2.680.33191380.24042184X-RAY DIFFRACTION99
2.68-2.780.30911440.23882192X-RAY DIFFRACTION98
2.78-2.910.27191420.2252168X-RAY DIFFRACTION98
2.91-3.060.29241410.23612164X-RAY DIFFRACTION97
3.06-3.260.26591480.24152189X-RAY DIFFRACTION98
3.26-3.510.25941370.22742183X-RAY DIFFRACTION98
3.51-3.860.25841490.21072222X-RAY DIFFRACTION98
3.86-4.420.22521410.18312176X-RAY DIFFRACTION98
4.42-5.560.23541430.17482226X-RAY DIFFRACTION99
5.57-39.230.22071390.21492265X-RAY DIFFRACTION98

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