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 SET7/9 IN COMPLEX WITH CYPROHEPTADINE
 
Authors :  H. Niwa, N. Handa, Y. Takemoto, A. Ito, Y. Tomabechi, T. Umehara, M. Shir M. Yoshida, S. Yokoyama
Date :  20 Aug 15  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Set Domain, Methyltransferase, Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Takemoto, A. Ito, H. Niwa, M. Okamura, T. Fujiwara, T. Hirano, N. Handa, T. Umehara, T. Sonoda, K. Ogawa, M. Tariq, N. Nishino, S. Dan, H. Kagechika, T. Yamori, S. Yokoyama, M. Yoshida
Identification Of Cyproheptadine As An Inhibitor Of Set Domain Containing Lysine Methyltransferase 7/9 (Set7/9) Tha Regulates Estrogen-Dependent Transcription
J. Med. Chem. V. 59 3650 2016
PubMed-ID: 27088648  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01732

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD7
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: CELL-FREE SYNTHESIS
    Expression System Plasmid: PX100709-08
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 111-366
    Gene: SETD7, KIAA1717, KMT7, SET7, SET9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H3-K4 METHYLTRANSFERASE SETD7,H3-K4-HMTASE SETD7, LYSINE N-METHYLTRANSFERASE 7,SET DOMAIN-CONTAINING PROTEIN 7,SET7/9

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1C7H1Ligand/Ion4-(DIBENZO[1,2-A:2',1'-D][7]ANNULEN-11-YLIDENE)-1-METHYL-PIPERIDINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4UNK6Mod. Amino Acid

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:223 , ALA A:226 , GLU A:228 , GLY A:264 , ASN A:265 , HIS A:293 , LYS A:294 , ALA A:295 , ASN A:296 , HIS A:297 , TYR A:335 , TRP A:352 , HOH A:534 , HOH A:579 , HOH A:581 , HOH A:588 , HOH A:626binding site for residue SAM A 401
2AC2SOFTWARETYR A:245 , ASN A:263 , GLY A:264 , THR A:266 , TYR A:305 , TYR A:335binding site for residue C7H A 402
3AC3SOFTWAREGLY A:237 , PRO A:238 , THR A:240 , ALA A:362 , THR A:363 , GLN A:365 , HOH A:523 , HOH A:533 , HOH A:604 , HOH A:609binding site for residue TRS A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:279 -Pro A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AYF)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeee........eeeeeee.....eeeeeeee..eeeeeeeeeeeeee..eeeeee.....ee.................hhhhhh.eeeee.......eeeee........eeeee..eeehhhhhhh.hhhhh...ee.....eee..............hhhhhee.....eeeeeeee...eeeeeeee........eeee..........hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ayf A 116 HGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGxxxxxxPEWYQVELKAFQATQQK 366
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335|||||||352       362    
                                                                                                                                                                                                                                                      336|||||||                
                                                                                                                                                                                                                                                       339-UNK||                
                                                                                                                                                                                                                                                        340-UNK|                
                                                                                                                                                                                                                                                         341-UNK                
                                                                                                                                                                                                                                                          342-UNK               
                                                                                                                                                                                                                                                           343-UNK              
                                                                                                                                                                                                                                                            344-UNK             
                                                                                                                                                                                                                                                             350
   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 5AYF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

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
    C7H  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:279 - Pro A:280   [ 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
  5ayf
    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
  SETD7_HUMAN | Q8WTS6
    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)
  2.1.1.43
    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
  SETD7_HUMAN | Q8WTS6
    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
        SETD7_HUMAN | Q8WTS6: 1h3i 1mt6 1muf 1n6a 1n6c 1o9s 1xqh 2f69 3cbm 3cbo 3cbp 3m53 3m54 3m55 3m56 3m57 3m58 3m59 3m5a 3os5 3vuz 3vv0 4e47 4j7f 4j7i 4j83 4j8o 4jds 4jlg 5eg2

(-) Related Entries Specified in the PDB File

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