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- PDB-7k2q: Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[Ahx-D... -

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Basic information

Entry
Database: PDB / ID: 7k2q
TitleKelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[Ahx-DPETGE]
Components
  • ACA-ASP-PRO-GLU-THR-GLY-GLU
  • Kelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / Peptide inhibitor / Inhibitor complex / Loop-mimic / cyclic peptide
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: 2.37 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_atom_id_1 / _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: ACA-ASP-PRO-GLU-THR-GLY-GLU


Theoretical massNumber of molelcules
Total (without water)64,2473
Polymers64,2473
Non-polymers00
Water2,540141
1
A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)31,7441
Polymers31,7441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11970 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
P: ACA-ASP-PRO-GLU-THR-GLY-GLU


Theoretical massNumber of molelcules
Total (without water)32,5032
Polymers32,5032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint4 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.150, 68.750, 77.595
Angle α, β, γ (deg.)90.000, 117.430, 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 ACA-ASP-PRO-GLU-THR-GLY-GLU


Mass: 759.759 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.: 141 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
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: 0.96707 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: 0.96707 Å / Relative weight: 1
ReflectionResolution: 2.37→42.12 Å / Num. obs: 29995 / % possible obs: 96.72 % / Redundancy: 5 % / Biso Wilson estimate: 46.78 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.09008 / Rpim(I) all: 0.04406 / Rrim(I) all: 0.1007 / Net I/σ(I): 8.32
Reflection shellResolution: 2.37→2.455 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4751 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 2636 / CC1/2: 0.821 / CC star: 0.95 / Rpim(I) all: 0.2696 / Rrim(I) all: 0.5507 / % possible all: 85.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFL

5wfl


Resolution: 2.37→42.12 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1990 6.63 %
Rwork0.2179 28005 -
obs0.2209 29995 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.06 Å2 / Biso mean: 46.7764 Å2 / Biso min: 16.85 Å2
Refinement stepCycle: final / Resolution: 2.37→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 0 141 4558
Biso mean---39.79 -
Num. residues----578
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 (%)
2.37-2.430.3411220.28311681180382
2.43-2.490.31651340.2861933206795
2.49-2.570.33511400.26882042218299
2.57-2.650.30921430.26572041218499
2.65-2.740.30291450.24852027217298
2.74-2.850.30921440.24612008215297
2.85-2.980.28161470.24541993214097
2.98-3.140.28741410.22842041218299
3.14-3.340.27841420.22612011215398
3.34-3.60.26341480.21841982213096
3.6-3.960.26771400.2072051219199
3.96-4.530.21911490.16962053220298
4.53-5.70.22331430.18542048219198
5.7-42.120.23851520.21962094224698

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