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(-) Description

Title :  THE FREE STRUCTURE OF THE MOUSE C-TERMINAL DOMAIN OF KDM6B
 
Authors :  J. Cheng, Z, D. J. Patel
Date :  01 May 12  (Deposition) - 08 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Jmjc Domain, Histone K27 Trimethyl And Dimethyl Demethylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kruidenier, C. W. Chung, Z. Cheng, J. Liddle, K. Che, G. Joberty, M. Bantscheff, C. Bountra, A. Bridges, H. Diallo, D. Eberhard, S. Hutchinson, E. Jones, R. Katso, M. Leveridge, P. K. Mander, J. Mosley, C. Ramirez-Molina, P. Rowland, C. J. Schofield, R. J. Sheppard, J. E. Smith, C. Swales, R. Tanner, P. Thomas, A. Tumber, G. Drewes, U. Oppermann, D. J. Patel, K. Lee, D. M. Wilson
A Selective Jumonji H3K27 Demethylase Inhibitor Modulates The Proinflammatory Macrophage Response.
Nature V. 488 404 2012
PubMed-ID: 22842901  |  Reference-DOI: 10.1038/NATURE11262

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 6B
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28 SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1155-1641
    Gene: KDM6B, JMJD3, KIAA0346
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: JMJC DOMAIN-CONTAINING PROTEIN 3, JUMONJI DOMAIN-CONTAINING PROTEIN 3

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2OGA2Ligand/IonN-OXALYLGLYCINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2OGA1Ligand/IonN-OXALYLGLYCINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:1381 , THR A:1387 , HIS A:1390 , GLU A:1392 , SER A:1398 , ASN A:1400 , HIS A:1470 , NI A:1701 , HOH A:1801 , HOH A:1827BINDING SITE FOR RESIDUE OGA A 1700
2AC2SOFTWAREHIS A:1390 , GLU A:1392 , HIS A:1470 , OGA A:1700 , HOH A:1827BINDING SITE FOR RESIDUE NI A 1701
3AC3SOFTWARECYS A:1575 , CYS A:1578 , CYS A:1602 , CYS A:1605BINDING SITE FOR RESIDUE ZN A 1702
4AC4SOFTWARELYS B:1381 , THR B:1387 , HIS B:1390 , GLU B:1392 , SER B:1398 , ASN B:1400 , HIS B:1470 , NI B:1701 , HOH B:1807 , HOH B:1832BINDING SITE FOR RESIDUE OGA B 1700
5AC5SOFTWAREHIS B:1390 , GLU B:1392 , HIS B:1470 , OGA B:1700 , HOH B:1832BINDING SITE FOR RESIDUE NI B 1701
6AC6SOFTWARECYS B:1575 , CYS B:1578 , CYS B:1602 , CYS B:1605BINDING SITE FOR RESIDUE ZN B 1702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EYU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:1404 -Pro A:1405
2Gly B:1404 -Pro B:1405

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EYU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EYU)

(-) Exons   (0, 0)

(no "Exon" information available for 4EYU)

(-) 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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh...........hhhhhh....eee..hhhhhhhhhhhhhhh.....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.........ee......ee..eeeee....eeehhhhhhhhh......eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4eyu A 1157 ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEELEVLFQHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSETYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296    ||1327      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587   || 1602      1612      1622      1632      
                                                                                                                                                                         1301|                                                                                                                                                                                                                                                                        1591|                                         
                                                                                                                                                                          1323                                                                                                                                                                                                                                                                         1597                                         


Chain B from PDB  Type:PROTEIN  Length:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.........hhhhhh....eee..hhhhhhhhhhhhhhh.....eeeeehhhhhh..hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeee.....eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.........ee......ee...eeeee..eeeehhhhhhhhh......eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4eyu B 1157 ESYLSPAQSVKPKINEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEELEVLFHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSETYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1166    ||1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298 ||   1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590||    1605      1615      1625      1635   
                                       1171|                                                                                                                          1300|                                                                                                                                                                                                                                                                        1591|                                         
                                        1174                                                                                                                           1323                                                                                                                                                                                                                                                                         1597
   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 4EYU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EYU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EYU)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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  4eyu
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  KDM6B_MOUSE | Q5NCY0
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM6B_MOUSE | Q5NCY0: 4ez4 4ezh

(-) Related Entries Specified in the PDB File

4ask KDM6B STRUCTURE BOUND WITH A HIGHLY SPECIFIC INHIBITOR
4ez4
4ezh