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- PDB-7k28: Kelch domain of human KEAP1 bound to Nrf2 peptide, ADEETGEFL -

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Basic information

Entry
Database: PDB / ID: 7k28
TitleKelch domain of human KEAP1 bound to Nrf2 peptide, ADEETGEFL
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2 peptide,ADEETGEFL
KeywordsPROTEIN BINDING / Peptide inhibitor / Inhibitor complex / Loop-mimic
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 / transcription regulator inhibitor activity / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / inclusion body / cellular response to interleukin-4 / regulation of autophagy ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / transcription regulator inhibitor activity / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / disordered domain specific binding / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / midbody / ubiquitin-dependent protein catabolic process / cellular response to oxidative stress / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / 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 / : / 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 ECH-associated protein 1 / : / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
P: Nrf2 peptide,ADEETGEFL


Theoretical massNumber of molelcules
Total (without water)64,5213
Polymers64,5213
Non-polymers00
Water00
1
A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)31,7441
Polymers31,7441
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11700 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
P: Nrf2 peptide,ADEETGEFL


Theoretical massNumber of molelcules
Total (without water)32,7782
Polymers32,7782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint1 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.008, 68.615, 77.350
Angle α, β, γ (deg.)90.000, 117.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31743.506 Da / Num. of mol.: 2
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 Nrf2 peptide,ADEETGEFL


Mass: 1034.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 2.95 Å3/Da / Density % sol: 58.24 %
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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.15→29.46 Å / Num. obs: 40840 / % possible obs: 99.67 % / Redundancy: 2 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03949 / Rpim(I) all: 0.03949 / Rrim(I) all: 0.05584 / Net I/σ(I): 11.35
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2963 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 3980 / CC1/2: 0.84 / CC star: 0.956 / Rpim(I) all: 0.2963 / Rrim(I) all: 0.4191 / % possible all: 98.08

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFL

5wfl


Resolution: 2.15→29.46 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 2007 4.91 %
Rwork0.2385 38832 -
obs0.2395 40839 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.78 Å2 / Biso mean: 45.5584 Å2 / Biso min: 18.05 Å2
Refinement stepCycle: final / Resolution: 2.15→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 0 0 4419
Num. residues----577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.32061280.30532556268493
2.2-2.260.32321490.283127642913100
2.26-2.330.34531400.297227532893100
2.33-2.40.28391450.283227772922100
2.4-2.490.35271390.299127572896100
2.49-2.590.32051490.295628172966100
2.59-2.710.34251370.293927472884100
2.71-2.850.28391410.270128212962100
2.85-3.030.27911490.262427522901100
3.03-3.260.29031450.260628182963100
3.26-3.590.23941440.241827732917100
3.59-4.10.23621460.203628022948100
4.1-5.170.18461480.167528252973100
5.17-29.460.24111470.227428703017100

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