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(-) 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 :  1.62
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
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODON PLUS RIL
    Fragment: UNP RESIDUES 1433-1711
    Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HIF-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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
176K1Ligand/Ion[(2~{S},5~{R})-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]-(3-OXIDANYLPROPYL)AZANIUM
2SCN2Ligand/IonTHIOCYANATE ION
3ZN3Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1499 , CYS A:1501 , CYS A:1516 , CYS A:1520binding site for residue ZN A 1801
2AC2SOFTWARECYS A:1516 , CYS A:1529 , CYS A:1533 , CYS A:1539 , SCN A:1804binding site for residue ZN A 1802
3AC3SOFTWARECYS A:1631 , CYS A:1678 , CYS A:1680 , CYS A:1685binding site for residue ZN A 1803
4AC4SOFTWAREMET A:1497 , GLN A:1498 , CYS A:1499 , ASN A:1522 , CYS A:1529 , SER A:1530 , CYS A:1533 , PRO A:1534 , ZN A:1802binding site for residue SCN A 1804
5AC5SOFTWAREASP A:1665 , TYR A:1666 , GLN A:1667 , PHE A:1668 , HOH A:1905 , HOH A:2086binding site for residue SCN A 1805
6AC6SOFTWAREGLY A:1434 , LYS A:1560 , GLY A:1561 , TRP A:1562 , TYR A:1579 , ILE A:1602 , HIS A:1603 , TYR A:1604 , TYR A:1605 , PHE A:1606 , ARG A:1625 , PHE A:1626 , MET A:1627 , ASN A:1628 , HIS A:1629 , TYR A:1666 , GLN A:1669 , LYS A:1677 , CYS A:1678 , PHE A:1679 , CYS A:1680 , HOH A:1946 , HOH A:1981 , HOH A:1991 , HOH A:2065binding site for residue 76K A 1806

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1449 -A:1463

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LSZ)

(-) 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:243
                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhh.......ee....ee...............hhhhhh.........hhhhh............eeeee.....eeeee........eeee...eeehhhhhhhhhhhhhhh......eeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee........eeee.hhhhhh...eee..........eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lsz A 1434 GETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLMQCECTPLIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRA 1699
                                  1443      1453      1463      1473      1497      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626      1636      1646      1656      1666      1676      1686      1696   
                                                                         1482|   1504|                                                                                                                                                                                         
                                                                          1497    1514
   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 5LSZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  SETD2_HUMAN | Q9BYW2
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 Related Entries

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

UniProtKB/Swiss-Prot
        SETD2_HUMAN | Q9BYW2: 2a7o 2mdc 2mdi 2mdj 4fmu 4h12 5jjy 5jlb 5jle 5lss 5lsx 5lsy 5lt6 5lt7 5lt8 5v21 5v22

(-) Related Entries Specified in the PDB File

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