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(-) Description

Title :  CRYSTAL STRUCTURE OF JMJD3 WITH GSK-J1
 
Authors :  C. Chung, J. Mosley, J. Liddle
Date :  01 May 12  (Deposition) - 25 Jul 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Kdm6B, Gsk-J1, Inhibitor, Lysine Specific Histone Demethylase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Kruidenier, C. 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
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC AND ZBD DOMAIN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJMJC DOMAIN-CONTAINING PROTEIN 3, JUMONJI DOMAIN-CONTAINING PROTEIN 3, LYSINE DEMETHYLASE 6B JMJD3

 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
1CO2Ligand/IonCOBALT (II) ION
2K0I2Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOICACID
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2K0I1Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOICACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2K0I1Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOICACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1575 , CYS A:1578 , CYS A:1602 , CYS A:1605BINDING SITE FOR RESIDUE ZN A2000
2AC2SOFTWAREHIS A:1390 , GLU A:1392 , HOH A:2327 , HOH A:2335 , K0I A:2639BINDING SITE FOR RESIDUE CO A3000
3AC3SOFTWARECYS B:1575 , CYS B:1578 , CYS B:1602 , CYS B:1605BINDING SITE FOR RESIDUE ZN B2000
4AC4SOFTWAREHIS B:1390 , GLU B:1392 , HOH B:2262 , HOH B:2270 , K0I B:2639BINDING SITE FOR RESIDUE CO B3000
5AC5SOFTWAREARG A:1246 , SER A:1270 , THR A:1330 , ASN A:1331 , TYR A:1379 , LYS A:1381 , ARG A:1386 , THR A:1387 , PRO A:1388 , HIS A:1390 , GLU A:1392 , ASN A:1393 , ASN A:1400 , ASN A:1480 , HOH A:2327 , HOH A:2335 , CO A:3000BINDING SITE FOR RESIDUE K0I A2639
6AC6SOFTWAREARG B:1246 , SER B:1270 , THR B:1330 , TYR B:1379 , LYS B:1381 , ARG B:1386 , THR B:1387 , PRO B:1388 , HIS B:1390 , GLU B:1392 , ASN B:1393 , ASN B:1400 , ASN B:1480 , HOH B:2262 , HOH B:2270 , CO B:3000BINDING SITE FOR RESIDUE K0I B2639

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ASK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM6B_HUMAN1339-1502
 
  2A:1339-1502
B:1339-1502
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM6B_HUMAN1339-1502
 
  1A:1339-1502
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM6B_HUMAN1339-1502
 
  1-
B:1339-1502

(-) Exons   (0, 0)

(no "Exon" information available for 4ASK)

(-) 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:428
 aligned with KDM6B_HUMAN | O15054 from UniProtKB/Swiss-Prot  Length:1643

    Alignment length:462
                                  1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626      1636  
         KDM6B_HUMAN   1177 PREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhh..hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhh------------------------------..eeeeeeeee......hhhhhhhhhhhhhhhh......hhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.........ee......ee..eeeeee.----..eeeehhhhhhhh.......eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:1339-1502 UniProt: 1339-1502                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ask A 1177 PREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESL------------------------------HHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSE----NTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286     |   -         -         -      1326      1336      1346      1356      1366      1376      1386      1396      1406      1416      1426      1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586    | 1596      1606      1616      1626      1636  
                                                                                                                                            1292                           1323                                                                                                                                                                                                                                                                        1591 1596                                          

Chain B from PDB  Type:PROTEIN  Length:423
 aligned with KDM6B_HUMAN | O15054 from UniProtKB/Swiss-Prot  Length:1643

    Alignment length:459
                                  1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599      1609      1619      1629         
         KDM6B_HUMAN   1180 KLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhh....eeeeehhhhhh..hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhh.------------------------------..eeeeeeeee......hhhhhhhhhhhhhhhh......hhhhh..........eeeee....eeeee.hhhhheeeeee.....eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.........ee......ee..eeeee.------..eeehhhhhhhh.......eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: B:1339-1502 UniProt: 1339-1502                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ask B 1180 KLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESL------------------------------HHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTS------TYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289  |      -         -         -   |  1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589|     1599      1609      1619      1629         
                                                                                                                                         1292                           1323                                                                                                                                                                                                                                                                       1590   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 4ASK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDM6B_HUMAN | O15054)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0071558    histone demethylase activity (H3-K27 specific)    Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0055007    cardiac muscle cell differentiation    The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0045446    endothelial cell differentiation    The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    GO:0071557    histone H3-K27 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
    GO:0016577    histone demethylation    The modification of histones by removal of methyl groups.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0002437    inflammatory response to antigenic stimulus    An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
    GO:0048333    mesodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0014823    response to activity    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
    GO:0060992    response to fungicide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fungicide stimulus. Fungicides are chemicals used to kill fungi.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM6B_HUMAN | O150542xue 2xxz 5fp3

(-) Related Entries Specified in the PDB File

2xue CRYSTAL STRUCTURE OF JMJD3
2xxz CRYSTAL STRUCTURE OF THE HUMAN JMJD3 JUMONJI DOMAIN