Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KEAP1 BTB DOMAIN IN COMPLEX WITH SMALL MOLECULE TX64014
 
Authors :  C. Huerta, X. Jiang, I. Trevino, C. F. Bender, K. K. Swinger, V. S. Stoll, D. A. Ferguson, P. J. Thomas, B. Probst, I. Dulubova, M. Visnick, W. C. W
Date :  19 Aug 15  (Deposition) - 10 Aug 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Keap1, Trascription Regulation, Btb Domain, Cysteine Modification, C1-(R)-Cys151 Adduct, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Huerta, X. Jiang, I. Trevino, C. F. Bender, D. A. Ferguson, B. Probst K. K. Swinger, V. S. Stoll, P. J. Thomas, I. Dulubova, M. Visnick, W. C. Wigley
Characterization Of Novel Small-Molecule Nrf2 Activators: Structural And Biochemical Validation Of Stereospecific Keap1 Binding.
Biochim. Biophys. Acta V. 1860 2537 2016
PubMed-ID: 27474998  |  Reference-DOI: 10.1016/J.BBAGEN.2016.07.026

(-) Compounds

Molecule 1 - KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BTB DOMAIN, RESIDUES 49-182
    Gene: KEAP1, INRF2, KIAA0132, KLHL19
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOSOLIC INHIBITOR OF NRF2,INRF2,KELCH-LIKE PROTEIN 19

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TX61Ligand/Ion(6AS,7S,10AS)-8-HYDROXY-4-METHOXY-2,7,10A-TRIMETHYL-5,6,6A,7,10,10A-HEXAHYDROBENZO[H]QUINAZOLINE-9-CARBONITRILE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TX62Ligand/Ion(6AS,7S,10AS)-8-HYDROXY-4-METHOXY-2,7,10A-TRIMETHYL-5,6,6A,7,10,10A-HEXAHYDROBENZO[H]QUINAZOLINE-9-CARBONITRILE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:85 , HIS A:129 , VAL A:132 , MET A:147 , GLY A:148 , LYS A:150 , CYS A:151 , HIS A:154binding site for residue TX6 A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DAD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DAD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DAD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DAD)

(-) Exons   (0, 0)

(no "Exon" information available for 5DAD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh.....eeeeee......eeeeehhhhhhh.hhhhhhhhh.eeeeee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dad A  50 RTFSYTLEDHTKQAFGIMNELRLSQQLCDVTLQVKYQDAPAAQFMAHKVVLASSSPVFKAMFTMEVVSIEGIHPKVMERLIEFAYTASISMGEKCVLHVMNGAVMYQIDSVVRACSDFLVQQL 179
                                    59        69        79        89        99       109  ||   126       136       146       156       166       176   
                                                                                        112|                                                           
                                                                                         120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DAD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DAD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DAD)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    TX6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dad)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5dad
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KEAP1_HUMAN | Q14145
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KEAP1_HUMAN | Q14145
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KEAP1_HUMAN | Q14145: 1u6d 1zgk 2flu 3vng 3vnh 3zgc 3zgd 4cxi 4cxj 4cxt 4ifj 4ifl 4ifn 4in4 4iqk 4l7b 4l7c 4l7d 4n1b 4xmb 5daf 5f72 5git 5nlb 5x54

(-) Related Entries Specified in the PDB File

5daf