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- PDB-7q96: Keap1 compound complex -

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Basic information

Entry
Database: PDB / ID: 7q96
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 / 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
Chem-9P0 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.415 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 12, 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

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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)64,7764
Polymers64,1302
Non-polymers6462
Water1,63991
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7113
Polymers32,0651
Non-polymers6462
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)75.868, 75.848, 204.332
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-9P0 / 4-[(5S,8R)-5-(dimethylcarbamoyl)-8-[[(2S)-1-ethanoylpyrrolidin-2-yl]carbonylamino]-7,11-bis(oxidanylidene)-10-oxa-3-thia-6-azabicyclo[10.4.0]hexadeca-1(16),12,14-trien-16-yl]benzoic acid


Mass: 610.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H34N4O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 91 / 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: 4.58 Å3/Da / Density % sol: 73.17 %
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: Apr 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→102.2 Å / Num. obs: 34145 / % possible obs: 72.3 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 14.6
Reflection shellResolution: 2.4→2.65 Å / Num. unique obs: 12071 / CC1/2: 0.5

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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: 2.415→102.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.274 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 1672 4.9 %RANDOM
Rwork0.195 ---
obs0.1961 34145 74 %-
Displacement parametersBiso max: 127.93 Å2 / Biso mean: 77.4 Å2 / Biso min: 52.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.9305 Å20 Å20 Å2
2--1.5399 Å20 Å2
3---0.3906 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.415→102.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 44 91 4507
Biso mean--88.42 68.59 -
Num. residues----570
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1486SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes797HARMONIC5
X-RAY DIFFRACTIONt_it4525HARMONIC10
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_contact3441SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4525HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6167HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion16.68
LS refinement shellResolution: 2.42→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3595 39 5.71 %
Rwork0.3207 644 -
all0.323 683 -
obs--8.88 %
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)
15.9150.98480.00722.98670.04861.9671-0.08150.59350.2766-0.11530.14960.0694-0.242-0.1646-0.0681-0.5222-0.00580.0401-0.377-0.059-0.5845-28.855522.6416-11.8843
23.4751.43270.67974.37780.48673.0290.2766-0.35140.00320.2446-0.3451-0.06510.1729-0.06720.0684-0.5448-0.05730.1374-0.6086-0.0554-0.6008-2.98919.5586-39.0129
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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