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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 :  06 Sep 16  (Deposition) - 05 Oct 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
176J2Ligand/Ion[(2~{S},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]-PENTYL-AZANIUM
2SCN2Ligand/IonTHIOCYANATE ION
3ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
176J1Ligand/Ion[(2~{S},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]-PENTYL-AZANIUM
2SCN1Ligand/IonTHIOCYANATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
176J1Ligand/Ion[(2~{S},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]-PENTYL-AZANIUM
2SCN1Ligand/IonTHIOCYANATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1631 , CYS A:1678 , CYS A:1680 , CYS A:1685binding site for residue ZN A 1801
02AC2SOFTWARECYS A:1516 , CYS A:1529 , CYS A:1533 , CYS A:1539binding site for residue ZN A 1802
03AC3SOFTWARECYS A:1499 , CYS A:1501 , CYS A:1516 , CYS A:1520binding site for residue ZN A 1803
04AC4SOFTWAREMET A:1497 , CYS A:1499 , ASN A:1522 , CYS A:1529 , SER A:1530 , CYS A:1533binding site for residue SCN A 1804
05AC5SOFTWARELYS A:1560 , GLY A:1561 , TRP A:1562 , TYR A:1579 , TYR A:1605 , SER A:1624 , ARG A:1625 , ASN A:1628 , HIS A:1629 , PHE A:1664 , TYR A:1666 , GLN A:1676 , LYS A:1677 , CYS A:1678 , PHE A:1679 , LEU A:1689 , HOH A:1922 , HOH A:1928binding site for residue 76J A 1805
06AC6SOFTWARECYS B:1499 , CYS B:1501 , CYS B:1516 , CYS B:1520binding site for residue ZN B 1801
07AC7SOFTWARECYS B:1516 , CYS B:1529 , CYS B:1533 , CYS B:1539binding site for residue ZN B 1802
08AC8SOFTWARECYS B:1631 , CYS B:1678 , CYS B:1680 , CYS B:1685binding site for residue ZN B 1803
09AC9SOFTWAREMET B:1497 , GLN B:1498 , CYS B:1499 , ASN B:1522 , CYS B:1529 , SER B:1530 , CYS B:1533binding site for residue SCN B 1804
10AD1SOFTWARELYS B:1560 , GLY B:1561 , TRP B:1562 , TYR B:1579 , TYR B:1605 , SER B:1624 , ARG B:1625 , MET B:1627 , ASN B:1628 , HIS B:1629 , TYR B:1666 , GLN B:1669 , GLN B:1676 , LYS B:1677 , CYS B:1678 , PHE B:1679 , HOH B:1918 , HOH B:1940 , HOH B:1941binding site for residue 76J B 1805

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LT6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LT6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LT6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LT6)

(-) Exons   (0, 0)

(no "Exon" information available for 5LT6)

(-) 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:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhhhhh.......ee....ee............hhhhhhh........hhhhhh.........hhhhh............eeeee.....eeeee........eeee...eeehhhhhhhhhhhhhhhh....eeeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee........eeeehhhhhee....ee..........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5lt6 A 1446 GPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLG 1690
                                  1455      1465      1475      1485|     1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626      1636      1646      1656      1666      1676      1686    
                                                                1485|                                                                                                                                                                                                 
                                                                 1497                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhh.......ee....ee...........hhhhhhh........hhhhhh.........hhhhh............eeeee.....eeeee........eeee...eeehhhhhhhhhhhhh........eeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee........eeeehhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lt6 B 1447 PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRAQKCFCGSANCRGYL 1689
                                  1456      1466      1476      1498      1508      1518      1528      1538      1548      1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668 ||   1682       
                                                             1483|                                                                                                                                                                          1670|              
                                                              1496                                                                                                                                                                           1675
   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 5LT6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LT6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LT6)

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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        SETD2_HUMAN | Q9BYW2: 2a7o 2mdc 2mdi 2mdj 4fmu 4h12 5jjy 5jlb 5jle 5lss 5lsx 5lsy 5lsz 5lt7 5lt8 5v21 5v22

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