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- PDB-6t7z: KEAP1 IN COMPLEX WITH COMPOUND 44 -

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Basic information

Entry
Database: PDB / ID: 6t7z
TitleKEAP1 IN COMPLEX WITH COMPOUND 44
Components
  • ACE-CYS-ASA-4FB-GLU-THR-GLY-GLU-CYS-NH2
  • Kelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / KEAP1 / UBIQUITINYLATION / INRF2 / KIAA0132 / KLHL19 / PROTEROS BIOSTRUCTURES GMBH
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 / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / regulation of autophagy / Ub-specific processing proteases / protein ubiquitination / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
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 / Kelch motif / 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 / Kelch motif / 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
ACETATE ION / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsColarusso, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Optimization of linear and cyclic peptide inhibitors of KEAP1-NRF2 protein-protein interaction.
Authors: Colarusso, S. / De Simone, D. / Frattarelli, T. / Andreini, M. / Cerretani, M. / Missineo, A. / Moretti, D. / Tambone, S. / Kempf, G. / Augustin, M. / Steinbacher, S. / Munoz-Sanjuan, I. / ...Authors: Colarusso, S. / De Simone, D. / Frattarelli, T. / Andreini, M. / Cerretani, M. / Missineo, A. / Moretti, D. / Tambone, S. / Kempf, G. / Augustin, M. / Steinbacher, S. / Munoz-Sanjuan, I. / Park, L. / Summa, V. / Tomei, L. / Bresciani, A. / Dominguez, C. / Toledo-Sherman, L. / Bianchi, E.
History
DepositionOct 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0May 24, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Jun 26, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.group_PDB ..._atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.1Nov 6, 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

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: ACE-CYS-ASA-4FB-GLU-THR-GLY-GLU-CYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0836
Polymers32,8472
Non-polymers2364
Water3,081171
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1885
Polymers31,9521
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACE-CYS-ASA-4FB-GLU-THR-GLY-GLU-CYS-NH2


Theoretical massNumber of molelcules
Total (without water)8951
Polymers8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.153, 75.153, 114.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-702-

ACT

21A-702-

ACT

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Components

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


Mass: 31951.773 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, RESIDUES 321-609
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 ACE-CYS-ASA-4FB-GLU-THR-GLY-GLU-CYS-NH2


Mass: 894.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2→65.08 Å / Num. obs: 25523 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 36.891 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.082 / Χ2: 1.016 / Net I/σ(I): 13.33
Reflection shellResolution: 2→2.25 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 13.33 / Num. unique obs: 121 / CC1/2: 0.995 / Rrim(I) all: 0.042 / % possible all: 97.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2→65.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.703 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1986 7.8 %RANDOM
Rwork0.2215 ---
obs0.2243 23535 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.42 Å2 / Biso mean: 39.394 Å2 / Biso min: 28.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0.82 Å20 Å2
2---1.65 Å20 Å2
3---2.47 Å2
Refinement stepCycle: final / Resolution: 2→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 77 171 2430
Biso mean--45.37 50.16 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192321
X-RAY DIFFRACTIONr_bond_other_d0.0020.021528
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9673159
X-RAY DIFFRACTIONr_angle_other_deg0.94533673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.63522.336107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19715330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6831523
X-RAY DIFFRACTIONr_chiral_restr0.0660.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 151 -
Rwork0.345 1596 -
all-1747 -
obs--99.89 %

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