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- PDB-7q6s: Keap1 compound complex -

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Basic information

Entry
Database: PDB / ID: 7q6s
TitleKeap1 compound complex
ComponentsKelch-like ECH-associated protein 1
KeywordsSTRUCTURAL PROTEIN / macrocycle 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 / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / 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
Chem-91M / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å
AuthorsJohansson, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction.
Authors: Begnini, F. / Geschwindner, S. / Johansson, P. / Wissler, L. / Lewis, R.J. / Danelius, E. / Luttens, A. / Matricon, P. / Carlsson, J. / Lenders, S. / Konig, B. / Friedel, A. / Sjo, P. / ...Authors: Begnini, F. / Geschwindner, S. / Johansson, P. / Wissler, L. / Lewis, R.J. / Danelius, E. / Luttens, A. / Matricon, P. / Carlsson, J. / Lenders, S. / Konig, B. / Friedel, A. / Sjo, P. / Schiesser, S. / Kihlberg, J.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7744
Polymers64,1302
Non-polymers6442
Water3,351186
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7093
Polymers32,0651
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)32,0651
Polymers32,0651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.400, 75.567, 202.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 32064.867 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: Chemical ChemComp-91M / (5S,8R)-16-(2,1,3-benzoxadiazol-4-yl)-8-[[(2S)-1-ethanoylpyrrolidin-2-yl]carbonylamino]-N,N-dimethyl-7,11-bis(oxidanylidene)-10-oxa-3-thia-6-azabicyclo[10.4.0]hexadeca-1(16),12,14-triene-5-carboxamide


Mass: 608.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N6O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 4.49 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown at 20 C in sitting drops using 200 nL of protein (11-13 mg/mL) and 200 nL of well solution (3.7-4.1 M ammonium acetate, 0.09 M sodium acetate pH 4.6 and 10 mM cadmium chloride).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.13→101.1 Å / Num. obs: 42464 / % possible obs: 65.8 % / Redundancy: 6.7 % / CC1/2: 1 / Net I/σ(I): 14
Reflection shellResolution: 2.13→2.37 Å / Num. unique obs: 15114 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (24-FEB-2021)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZGK

1zgk


Resolution: 2.143→101.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2122 5 %RANDOM
Rwork0.2106 ---
obs0.2116 42464 66 %-
Displacement parametersBiso max: 110.78 Å2 / Biso mean: 66.29 Å2 / Biso min: 45.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.7691 Å20 Å20 Å2
2--0.3721 Å20 Å2
3---2.397 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.143→101.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 44 186 4602
Biso mean--82.76 65.51 -
Num. residues----570
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1485SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes796HARMONIC5
X-RAY DIFFRACTIONt_it4526HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion561SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3571SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4526HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6169HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion16.76
LS refinement shellResolution: 2.143→2.31 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3352 49 5.76 %
Rwork0.3006 801 -
obs--6.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.15140.76610.00162.00170.10781.2078-0.11810.45690.2142-0.19930.12590.0488-0.1888-0.0765-0.0078-0.3177-0.02620.0208-0.1886-0.072-0.2899-29.139422.4362-11.8571
22.40021.29620.4882.93750.46322.15180.1976-0.27130.00560.0829-0.2976-0.05660.1274-0.07770.1-0.3133-0.04410.1176-0.3995-0.0451-0.3062-3.1519.273-38.5737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A325 - 609
2X-RAY DIFFRACTION2{ B|* }B325 - 609

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