[English] 日本語
Yorodumi
- PDB-4in4: Crystal structure of cpd 15 bound to Keap1 Kelch domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4in4
TitleCrystal structure of cpd 15 bound to Keap1 Kelch domain
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION
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-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 / 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 / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-4ID / PHOSPHATE ION / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSilvian, L. / Marcotte, D.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Small molecules inhibit the interaction of Nrf2 and the Keap1 Kelch domain through a non-covalent mechanism.
Authors: Marcotte, D. / Zeng, W. / Hus, J.C. / McKenzie, A. / Hession, C. / Jin, P. / Bergeron, C. / Lugovskoy, A. / Enyedy, I. / Cuervo, H. / Wang, D. / Atmanene, C. / Roecklin, D. / Vecchi, M. / ...Authors: Marcotte, D. / Zeng, W. / Hus, J.C. / McKenzie, A. / Hession, C. / Jin, P. / Bergeron, C. / Lugovskoy, A. / Enyedy, I. / Cuervo, H. / Wang, D. / Atmanene, C. / Roecklin, D. / Vecchi, M. / Vivat, V. / Kraemer, J. / Winkler, D. / Hong, V. / Chao, J. / Lukashev, M. / Silvian, L.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,78117
Polymers98,0363
Non-polymers3,74514
Water2,972165
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0537
Polymers32,6791
Non-polymers1,3756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9586
Polymers32,6791
Non-polymers1,2805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7694
Polymers32,6791
Non-polymers1,0903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.604, 96.509, 142.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Detailsbiological unit is a monomer

-
Components

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


Mass: 32678.564 Da / Num. of mol.: 3 / Fragment: Kelch domain residues 321-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INRF2, KEAP1, KIAA0132, KLHL19 / Plasmid: pET28b(+) / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21 Codon Plus(DE3)-RIL / References: UniProt: Q14145
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-4ID / 2-({5-[(2,4-dimethylphenyl)sulfonyl]-6-oxo-1,6-dihydropyrimidin-2-yl}sulfanyl)-N-[2-(trifluoromethyl)phenyl]acetamide


Mass: 497.511 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H18F3N3O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5M Sodium Formate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 23, 2010 / Details: MONOCHROMATOR
RadiationMonochromator: Kohzu HLD-4 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.59→96.7 Å / Num. all: 35183 / Num. obs: 35183 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.2 / Rsym value: 0.189 / Net I/σ(I): 9.5
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5054 / Rsym value: 0.722 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zgk

1zgk


Resolution: 2.59→96.51 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 9.411 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.577 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 1764 5 %RANDOM
Rwork0.1908 ---
obs0.1937 33363 99.92 %-
all-35130 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.35 Å2 / Biso mean: 22.6175 Å2 / Biso min: 4.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.04 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.59→96.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 238 165 7007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197007
X-RAY DIFFRACTIONr_bond_other_d0.0010.026213
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9749578
X-RAY DIFFRACTIONr_angle_other_deg0.873314167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30522.593324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60515982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7621566
X-RAY DIFFRACTIONr_chiral_restr0.0950.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218131
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021763
X-RAY DIFFRACTIONr_mcbond_it1.5332.13441
X-RAY DIFFRACTIONr_mcbond_other1.5332.13440
X-RAY DIFFRACTIONr_mcangle_it2.5383.1454296
LS refinement shellResolution: 2.594→2.661 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 121 -
Rwork0.236 2431 -
all-2552 -
obs-2552 100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more