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 :  STRUCTURE OF THE EPIGENETIC ONCOGENE MMSET AND INHIBITION BY N-ALKYL SINEFUNGIN DERIVATIVES
 
Authors :  D. Tisi, P. Pathuri, T. Heightman
Date :  05 Sep 16  (Deposition) - 05 Oct 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Lysine Methyltransferase Setd2 Set Domain, Setd2#1, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Tisi, E. Chiarparin, E. Tamanini, P. Pathuri, J. E. Coyle, A. Hold, F. P. Holding, N. Amin, A. C. Martin, S. J. Rich, V. Berdini, J. Yon, P. Acklam, R. Burke, L. Drouin, J. E. Harmer, F. Jeganathan, R. L. Van Montfort, Y. Newbatt, M. Tortorici, M. Westlake, A. Wood, S. Hoelder, T. D. Heightman
Structure Of The Epigenetic Oncogene Mmset And Inhibition B N-Alkyl Sinefungin Derivatives.
Acs Chem. Biol. V. 11 3093 2016
PubMed-ID: 27571355  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00308

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD2
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    Expression System VariantCODON PLUS RIL
    FragmentUNP RESIDUES 1433-1711
    GeneSETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHIF-1,HUNTINGTIN YEAST PARTNER B,HUNTINGTIN-INTERACTING PROTEIN 1,HIP-1,HUNTINGTIN-INTERACTING PROTEIN B,LYSINE N- METHYLTRANSFERASE 3A,SET DOMAIN-CONTAINING PROTEIN 2,HSET2,P231HBP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
176O1Ligand/Ion[(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]-5-AZANIUMYL-6-OXIDANYL-6-OXIDANYLIDENE-HEXAN-2-YL]-(PHENYLMETHYL)AZANIUM
2ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1631 , CYS A:1678 , CYS A:1680 , CYS A:1685binding site for residue ZN A 1801
2AC2SOFTWARECYS A:1499 , CYS A:1501 , CYS A:1516 , CYS A:1520binding site for residue ZN A 1802
3AC3SOFTWARECYS A:1516 , CYS A:1529 , CYS A:1533 , CYS A:1539binding site for residue ZN A 1803
4AC4SOFTWARELYS A:1560 , GLY A:1561 , TRP A:1562 , TYR A:1579 , HIS A:1603 , TYR A:1604 , TYR A:1605 , PHE A:1606 , ARG A:1625 , MET A:1627 , ASN A:1628 , HIS A:1629 , PHE A:1650 , TYR A:1666 , GLN A:1676 , LYS A:1677 , PHE A:1679 , CYS A:1680binding site for residue 76O A 1804

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LSX)

(-) 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:231
                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh.......ee.................hhhhhhh........hhhhhh..........................eeeee.....eeeee........eeee...eeehhhhhhhhhhhhhhhh.....eeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee..........ee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lsx A 1446 GPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTEMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQREAQKCFCGSANCRGYLGG 1691
                                  1455      1465      1475      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587      1597      1607      1617      1627      1637      1647      1657      1667  ||  1680      1690 
                                                               1484|                                                                                                                                                                         1670|                 
                                                                1497                                                                                                                                                                          1674                 

   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 5LSX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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
    76O  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5lsx)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5lsx
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SETD2_HUMAN | Q9BYW2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.43
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SETD2_HUMAN | Q9BYW2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SETD2_HUMAN | Q9BYW22a7o 2mdc 2mdi 2mdj 4fmu 4h12 5jjy 5jlb 5jle 5lss 5lsy 5lsz 5lt6 5lt7 5lt8 5v21 5v22

(-) Related Entries Specified in the PDB File

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