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- PDB-5git: BTB domain of KEAP1 in complex with XX3 -

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Basic information

Entry
Database: PDB / ID: 5git
TitleBTB domain of KEAP1 in complex with XX3
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / SIGNALING PROTEIN
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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-XXT / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.19 Å
AuthorsZhu, L.L. / Li, H.L. / Wu, F.S. / Xiong, R.
CitationJournal: Antioxid. Redox Signal. / Year: 2017
Title: Britanin Ameliorates Cerebral Ischemia-Reperfusion Injury by Inducing the Nrf2 Protective Pathway.
Authors: Wu, G.Z. / Zhu, L.L. / Yuan, X. / Chen, H. / Xiong, R. / Zhang, S.D. / Cheng, H. / Shen, Y.H. / An, H.Z. / Li, T.J. / Li, H.L. / Zhang, W.D.
History
DepositionJun 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6602
Polymers15,2941
Non-polymers3661
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8670 Å2
Unit cell
Length a, b, c (Å)42.450, 42.450, 265.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Keap 1


Mass: 15293.651 Da / Num. of mol.: 1 / Fragment: BTB, UNP residues 48-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical ChemComp-XXT / [(3aS,5R,5aS,6S,8S,8aS,9S,9aR)-9-acetyloxy-8-hydroxy-5,8a-dimethyl-1-methylidene-2-oxo-4,5,5a,6,7,8,9,9a-octahydro-3aH-azuleno[6,5-b]furan-6-yl] acetate / Britannin


Mass: 366.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M lithium acetate, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.19→36.76 Å / Num. obs: 8098 / % possible obs: 99.5 % / Redundancy: 11.8 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.19→36.76 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.833 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27809 439 5.4 %RANDOM
Rwork0.21631 ---
obs0.21969 7638 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.19→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 26 32 1072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191060
X-RAY DIFFRACTIONr_bond_other_d0.0010.021025
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9821435
X-RAY DIFFRACTIONr_angle_other_deg0.8913.0012355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5892546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68415186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.534154
X-RAY DIFFRACTIONr_chiral_restr0.1030.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0865.402519
X-RAY DIFFRACTIONr_mcbond_other5.0465.398518
X-RAY DIFFRACTIONr_mcangle_it7.6068.06647
X-RAY DIFFRACTIONr_mcangle_other7.6098.068648
X-RAY DIFFRACTIONr_scbond_it5.7586.258540
X-RAY DIFFRACTIONr_scbond_other5.7546.267541
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.79.126789
X-RAY DIFFRACTIONr_long_range_B_refined11.04642.0381166
X-RAY DIFFRACTIONr_long_range_B_other11.04742.11167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 27 -
Rwork0.238 561 -
obs--100 %

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