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- PDB-7k2o: Kelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c... -

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Basic information

Entry
Database: PDB / ID: 7k2o
TitleKelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c[GABA-DPETGE]
Components
  • (ABU)DPETGE
  • Kelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING/Inhibitor / Peptide inhibitor / Inhibitor complex / Loop-mimic / PROTEIN BINDING / cyclic peptide / PROTEIN BINDING-Inhibitor complex
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / 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 repeat type 1 / Kelch motif / 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 repeat type 1 / Kelch motif / 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: 2.11 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

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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: (ABU)DPETGE


Theoretical massNumber of molelcules
Total (without water)66,9763
Polymers66,9763
Non-polymers00
Water2,270126
1
A: Kelch-like ECH-associated protein 1
P: (ABU)DPETGE


Theoretical massNumber of molelcules
Total (without water)33,8542
Polymers33,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint0 kcal/mol
Surface area11710 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)33,1221
Polymers33,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.286, 68.803, 77.098
Angle α, β, γ (deg.)90.000, 117.588, 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: 33122.000 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 (ABU)DPETGE


Mass: 731.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.08 %
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: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.108→29.33 Å / Num. obs: 43354 / % possible obs: 99.27 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.71 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03772 / Rpim(I) all: 0.03772 / Rrim(I) all: 0.05335 / Net I/σ(I): 11.03
Reflection shellResolution: 2.108→2.183 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2884 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 4153 / CC1/2: 0.878 / CC star: 0.967 / Rpim(I) all: 0.2884 / Rrim(I) all: 0.4078 / % possible all: 95.75

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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: 2.11→29.33 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 2004 4.63 %
Rwork0.2083 41321 -
obs0.2101 43325 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.86 Å2
Refinement stepCycle: LAST / Resolution: 2.11→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4446 0 0 126 4572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844556
X-RAY DIFFRACTIONf_angle_d1.05016203
X-RAY DIFFRACTIONf_chiral_restr0.0615663
X-RAY DIFFRACTIONf_plane_restr0.006819
X-RAY DIFFRACTIONf_dihedral_angle_d15.935659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.28641410.26972806X-RAY DIFFRACTION94.33
2.16-2.220.31011430.26272918X-RAY DIFFRACTION99.64
2.22-2.280.29251430.25382951X-RAY DIFFRACTION99.61
2.28-2.360.26961430.24422930X-RAY DIFFRACTION99.68
2.36-2.440.34431480.25472942X-RAY DIFFRACTION99.65
2.44-2.540.34371390.25522963X-RAY DIFFRACTION99.77
2.54-2.660.27641460.24742954X-RAY DIFFRACTION99.94
2.66-2.80.27331340.22792961X-RAY DIFFRACTION99.61
2.8-2.970.2571370.22192964X-RAY DIFFRACTION99.74
2.97-3.20.25491440.21952952X-RAY DIFFRACTION99.9
3.2-3.520.23761420.21252976X-RAY DIFFRACTION99.71
3.52-4.030.20931470.18552981X-RAY DIFFRACTION99.78
4.03-5.070.20421470.1572970X-RAY DIFFRACTION99.62
5.07-29.330.24291500.20553053X-RAY DIFFRACTION99.5

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