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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE AHR-ARNT HETERODIMER IN COMPLEX WITH THE DRE
 
Authors :  S. -H. Seok, W. Lee, L. Jiang, C. A. Bradfield, Y. Xing
Date :  28 Feb 17  (Deposition) - 19 Apr 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ahr, Arnt, Transcription Factor, Heterodimer, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Seok, W. Lee, L. Jiang, K. Molugu, A. Zheng, Y. Li, S. Park, C. A. Bradfield, Y. Xing
Structural Hierarchy Controlling Dimerization And Target Dn Recognition In The Ahr Transcriptional Complex.
Proc. Natl. Acad. Sci. V. 114 5431 2017 U. S. A.
PubMed-ID: 28396409  |  Reference-DOI: 10.1073/PNAS.1617035114

(-) Compounds

Molecule 1 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARNT, BHLHE2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARNT PROTEIN,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 2, BHLHE2,DIOXIN RECEPTOR,NUCLEAR TRANSLOCATOR,HYPOXIA-INDUCIBLE FACTOR 1-BETA,HIF1-BETA
 
Molecule 2 - ARYL HYDROCARBON RECEPTOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AHR
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: AHR
 
Molecule 3 - DNA (5'- D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')
    Chains: C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')
    Chains: D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:161 , THR B:162 , GLU B:163binding site for residue CIT B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V0L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro B:203 -Pro B:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V0L)

(-) Exons   (0, 0)

(no "Exon" information available for 5V0L)

(-) Sequences/Alignments

Asymmetric/Biological 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee......eee........hhhhhhh.hhhhhhhhhhh...........eee..............eee...............ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v0l A  81 QSSADKERLARENHSEIERRRRNKMTAYITELSDMVPTCSALARKPDKLTILRMAVSHMKSLKPSFLTDQELKHLILEAADGFLFIVSCETGRVVYVSDSVTPQPQSEWFGSTLYDQVHPDDVDKLREQLSGSRRSFICRMRCEPHFVVVHCTGYDDDPEAGQGSKFCLVAIGRLQ 344
                                    90       100       110       120       130       140 ||    162       172       182       192  ||   205       215       225||     266  ||   306    || 328       338      
                                                                                       142|                                     195|                        226|        269|        311|                    
                                                                                        155                                      199                         258         300         324                    


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh............hhhhhh..eee...................hhhhhh...hhhhh...hhhhhhhhhhh...........ee..ee.......ee..eeeeeee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v0l B  37 RHRDRLNTELDRLASLLPFPQDVINKLDKLSVLRLSVSYLRAKSFFDVALKSTQEGEFLLQALVLVVTADALVFYASSTIQDYLGFQQSDVIHQSVYELIHTEDRAEFQRQLHWALDQLPPENASFMERCFRCDNSSGFLAMNFQGRLKYLHLPPQLALFAIATPL 266
                                    46        56        66        76        86  ||   117  ||   130       140       150       160       170     ||203       213  ||   229       239 ||    260      
                                                                               89|      120|                                                 176|             216|               241|             
                                                                               111       124                                                  200              223                253             


Chain C from PDB  Type:DNA  Length:17
                                                 
                 5v0l C   4 GGATTGCGTGAGAACTG  20
                                    13       


Chain D from PDB  Type:DNA  Length:14
                                              
                 5v0l D   4 AGTTCTCACGCAAT  17
                                    13
   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 5V0L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V0L)

(-) Gene Ontology  (94, 112)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro B:203 - Pro B:204   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  5v0l
    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
  AHR_MOUSE | P30561
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ARNT_HUMAN | P27540
    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
  AHR_MOUSE | P30561
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ARNT_HUMAN | P27540
    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
        AHR_MOUSE | P30561: 4m4x
        ARNT_HUMAN | P27540: 1d7g 1x0o 2a24 2arn 2b02 2hv1 2k7s 3f1n 3f1o 3f1p 3h7w 3h82 4eq1 4ghi 4gs9 4h6j 4lpz 4pky 4xt2 5nj8 5tbm 5ufp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5V0L)