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- PDB-8ehv: Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[DhA-G... -

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Basic information

Entry
Database: PDB / ID: 8ehv
TitleKelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[DhA-GDPET(bAla)E]
Components
  • Kelch-like ECH-associated protein 1
  • cyclic peptide c[DhA-GDPET(bAla)E
KeywordsPROTEIN BINDING / Protein-protein interaction / inhibitor
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 / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / regulation of autophagy / protein ubiquitination / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytoplasm / cytosol
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 motif / Kelch / 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 motif / Kelch / 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: 2.29 Å
AuthorsMuellers, S.N. / Allen, K.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Machine-learning analysis of molecular dynamics simulations to elucidate the effect of strain and preorganization on conformational modes of motion in cyclic peptides
Authors: Muellers, S.N. / Allen, K.N. / Whitty, A.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_rmsd_angle
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_chiral.auth_atom_id / _pdbx_validate_close_contact.auth_atom_id_1

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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: cyclic peptide c[DhA-GDPET(bAla)E


Theoretical massNumber of molelcules
Total (without water)74,5443
Polymers74,5443
Non-polymers00
Water3,423190
1
A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)36,8991
Polymers36,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
P: cyclic peptide c[DhA-GDPET(bAla)E


Theoretical massNumber of molelcules
Total (without water)37,6452
Polymers37,6452
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-1 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.349, 68.849, 77.215
Angle α, β, γ (deg.)90.00, 117.63, 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: 36899.176 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 cyclic peptide c[DhA-GDPET(bAla)E


Mass: 745.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1.2-1.6 M ammonium sulfate, 100 mM Bis-Tris pH 6.5, 0.2-0.8% PEG-550 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.29→29.58 Å / Num. obs: 34135 / % possible obs: 99.75 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.063 / Rrim(I) all: 0.164 / Net I/σ(I): 11.2
Reflection shellResolution: 2.29→2.372 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3336 / CC1/2: 0.761 / Rpim(I) all: 0.381 / Rrim(I) all: 0.973 / % possible all: 99.31

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFV

5wfv


Resolution: 2.29→29.58 Å / SU ML: 0.319 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.808
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.253 1996 5.85 %
Rwork0.203 --
obs0.206 34135 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.59 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 190 4608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194523
X-RAY DIFFRACTIONf_angle_d1.756157
X-RAY DIFFRACTIONf_dihedral_angle_d21.3441607
X-RAY DIFFRACTIONf_chiral_restr0.097660
X-RAY DIFFRACTIONf_plane_restr0.01811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.340.33541280.27142122X-RAY DIFFRACTION92
2.34-2.410.29661450.25372289X-RAY DIFFRACTION100
2.41-2.480.33491370.25762283X-RAY DIFFRACTION100
2.48-2.560.33221400.23832296X-RAY DIFFRACTION100
2.56-2.650.29441500.22912309X-RAY DIFFRACTION100
2.65-2.750.27981390.2222304X-RAY DIFFRACTION100
2.75-2.880.26881410.22342296X-RAY DIFFRACTION100
2.88-3.030.26871430.21542284X-RAY DIFFRACTION100
3.03-3.220.26831400.21342316X-RAY DIFFRACTION100
3.22-3.470.24371440.21062304X-RAY DIFFRACTION100
3.47-3.820.25281490.18852315X-RAY DIFFRACTION100
3.82-4.370.21951450.16692319X-RAY DIFFRACTION100
4.37-5.50.18461450.15992336X-RAY DIFFRACTION100
5.5-29.580.27141500.21972366X-RAY DIFFRACTION100

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