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- PDB-6fmq: Keap1 - peptide complex -

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Basic information

Entry
Database: PDB / ID: 6fmq
TitleKeap1 - peptide complex
Components
  • ACY-SC1-GLU-THR-GLY-GLU-LEU
  • Kelch-like ECH-associated protein 1
KeywordsPEPTIDE BINDING PROTEIN / Keap1 / Kelch-domain / Nrf2 / Neurodegenerative / 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 / ubiquitin-dependent protein catabolic process / midbody / 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-type beta propeller / 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-type beta propeller / 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. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
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: 2.1 Å
AuthorsTalapatra, S.K. / Kozielski, F. / Wells, G. / Georgakopoulos, N.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UCL Secondment MRC PtD530912 United Kingdom
CitationJournal: Chembiochem / Year: 2018
Title: Modified Peptide Inhibitors of the Keap1-Nrf2 Protein-Protein Interaction Incorporating Unnatural Amino Acids.
Authors: Georgakopoulos, N.D. / Talapatra, S.K. / Gatliff, J. / Kozielski, F. / Wells, G.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
D: ACY-SC1-GLU-THR-GLY-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,31721
Polymers92,4943
Non-polymers82318
Water6,413356
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-65 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.652, 76.129, 211.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABD

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


Mass: 45854.258 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 ACY-SC1-GLU-THR-GLY-GLU-LEU


Mass: 785.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 374 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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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: 4.75 Å3/Da / Density % sol: 74.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4.0 M ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 71681 / % possible obs: 99.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.21 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNG

3vng


Resolution: 2.1→47.837 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.1997 3639 5.09 %
Rwork0.1654 --
obs0.1671 71513 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 107 356 4844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124725
X-RAY DIFFRACTIONf_angle_d1.2036437
X-RAY DIFFRACTIONf_dihedral_angle_d8.7853621
X-RAY DIFFRACTIONf_chiral_restr0.086676
X-RAY DIFFRACTIONf_plane_restr0.007868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12760.30671430.25682536X-RAY DIFFRACTION99
2.1276-2.15680.29281330.252618X-RAY DIFFRACTION100
2.1568-2.18760.26411420.2482569X-RAY DIFFRACTION99
2.1876-2.22020.26561350.24922540X-RAY DIFFRACTION98
2.2202-2.25490.28721330.23612553X-RAY DIFFRACTION98
2.2549-2.29190.24891190.22452628X-RAY DIFFRACTION100
2.2919-2.33140.26491080.21992593X-RAY DIFFRACTION100
2.3314-2.37380.27731440.20922612X-RAY DIFFRACTION100
2.3738-2.41950.23781380.2032592X-RAY DIFFRACTION100
2.4195-2.46880.27151020.21012642X-RAY DIFFRACTION100
2.4688-2.52250.24921500.21162589X-RAY DIFFRACTION100
2.5225-2.58120.25141480.21222592X-RAY DIFFRACTION100
2.5812-2.64570.27061420.20212600X-RAY DIFFRACTION100
2.6457-2.71730.25081600.20372590X-RAY DIFFRACTION100
2.7173-2.79720.25331530.19522573X-RAY DIFFRACTION99
2.7972-2.88750.2261480.17682527X-RAY DIFFRACTION97
2.8875-2.99070.18911170.18032628X-RAY DIFFRACTION99
2.9907-3.11040.20231290.18812620X-RAY DIFFRACTION100
3.1104-3.25190.24251420.17792638X-RAY DIFFRACTION100
3.2519-3.42330.17741390.16152619X-RAY DIFFRACTION100
3.4233-3.63770.1941430.1492631X-RAY DIFFRACTION99
3.6377-3.91850.16311420.13722620X-RAY DIFFRACTION99
3.9185-4.31260.14511530.11852640X-RAY DIFFRACTION99
4.3126-4.93610.11581560.11092641X-RAY DIFFRACTION99
4.9361-6.21680.19871330.14382686X-RAY DIFFRACTION98
6.2168-47.8490.22321870.1742797X-RAY DIFFRACTION99

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