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- PDB-7k2k: Kelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[BAL-D... -

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Basic information

Entry
Database: PDB / ID: 7k2k
TitleKelch domain of human KEAP1 bound to Nrf2 cyclic peptide, c[BAL-DEETGE]
Components
  • BAL-ASP-GLU-GLU-THR-GLY-GLU
  • 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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: BAL-ASP-GLU-GLU-THR-GLY-GLU


Theoretical massNumber of molelcules
Total (without water)66,7623
Polymers66,7623
Non-polymers00
Water4,756264
1
A: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)33,0061
Polymers33,0061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
P: BAL-ASP-GLU-GLU-THR-GLY-GLU


Theoretical massNumber of molelcules
Total (without water)33,7562
Polymers33,7562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint1 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.552, 68.874, 77.470
Angle α, β, γ (deg.)90.000, 117.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-770-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 327 through 348 or (resid 349...
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUSERSER(chain A and (resid 327 through 348 or (resid 349...AA327 - 3484 - 25
12ASPASPASPASP(chain A and (resid 327 through 348 or (resid 349...AA34926
13LEULEUARGARG(chain A and (resid 327 through 348 or (resid 349...AA327 - 6144 - 291
14LEULEUARGARG(chain A and (resid 327 through 348 or (resid 349...AA327 - 6144 - 291
15LEULEUARGARG(chain A and (resid 327 through 348 or (resid 349...AA327 - 6144 - 291
16LEULEUARGARG(chain A and (resid 327 through 348 or (resid 349...AA327 - 6144 - 291
21LEULEUTHRTHRchain BBB327 - 6094 - 286

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Components

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


Mass: 33005.934 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 BAL-ASP-GLU-GLU-THR-GLY-GLU


Mass: 749.678 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.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.04 Å3/Da / Density % sol: 59.54 %
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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→29.37 Å / Num. obs: 51638 / % possible obs: 94.53 % / Redundancy: 5.1 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07087 / Rpim(I) all: 0.03433 / Rrim(I) all: 0.079 / Net I/σ(I): 8.55
Reflection shellResolution: 1.982→2.053 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.4611 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 3950 / CC1/2: 0.829 / CC star: 0.952 / Rpim(I) all: 0.2307 / Rrim(I) all: 0.5175 / % possible all: 75.25

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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: 1.98→29.37 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 2006 4.02 %
Rwork0.197 47896 -
obs0.1979 49902 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.9 Å2 / Biso mean: 37.7873 Å2 / Biso min: 11.87 Å2
Refinement stepCycle: final / Resolution: 1.98→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 0 264 4687
Biso mean---34 -
Num. residues----578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2537X-RAY DIFFRACTION6.651TORSIONAL
12B2537X-RAY DIFFRACTION6.651TORSIONAL
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 (%)
1.98-2.030.27461110.2262631274273
2.03-2.090.21781350.23172932306782
2.09-2.150.29021370.22783377351494
2.15-2.220.24791470.21693543369098
2.22-2.30.2661460.21033513365998
2.3-2.390.21191480.20893530367898
2.39-2.50.2281420.22373481362397
2.5-2.630.28081450.21983484362996
2.63-2.790.23831500.20583553370399
2.79-3.010.22761490.19963566371599
3.01-3.310.26491480.20493487363596
3.31-3.790.21271450.18983607375299
3.79-4.770.15291540.15453563371798
4.77-29.370.19691490.19173629377897

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