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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN JMJD3 JUMONJI DOMAIN
 
Authors :  K. H. Che, W. W. Yue, T. Krojer, J. R. C. Muniz, S. S. Ng, A. Tumber, M. Danie N. Burgess-Brown, P. Savitsky, E. Ugochukwu, P. Filippakopoulos, C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Date :  12 Nov 10  (Deposition) - 24 Nov 10  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Histone Demethylation, Oxygenase, Chromatin Modification (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. H. Che, W. W. Yue, T. Krojer, J. R. C. Muniz, S. S. Ng, A. Tumber, M. Daniel, N. Burgess-Brown, P. Savitsky, F. Von Delft, E. Ugochukwu P. Filippakopoulos, C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Crystal Structure Of The Human Jmjd3 Jumonji Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 6B
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-PRARE2
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentJUMONJI DOMAIN, RESIDUES 1173-1502
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJMJD3, JMJC DOMAIN-CONTAINING PROTEIN 3, JUMONJI DOMAIN-CONTAINING PROTEIN 3, LYSINE DEMETHYLASE 6B

 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  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
18XQ2Ligand/Ion8-HYDROXYQUINOLINE-5-CARBOXYLIC ACID
2EDO5Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
4NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
18XQ1Ligand/Ion8-HYDROXYQUINOLINE-5-CARBOXYLIC ACID
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION
4NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
18XQ1Ligand/Ion8-HYDROXYQUINOLINE-5-CARBOXYLIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION
4NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:1387 , GLU A:1389 , HOH A:2098 , HOH A:2103 , 8XQ A:3001BINDING SITE FOR RESIDUE NI A2494
02AC2SOFTWAREHOH A:2013 , HOH A:2015 , HOH A:2054 , HOH A:2059 , HOH A:2060 , HOH B:2150BINDING SITE FOR RESIDUE NI A2500
03AC3SOFTWAREHIS B:1387 , GLU B:1389 , HOH B:2083 , HOH B:2155 , 8XQ B:3001BINDING SITE FOR RESIDUE NI B2500
04AC4SOFTWAREGLU A:1287 , GLU B:1188 , HOH B:2011 , HOH B:2012 , HOH B:2013BINDING SITE FOR RESIDUE NA A2495
05AC5SOFTWAREILE A:1185 , TYR A:1186 , GLN B:1200 , HOH B:2020BINDING SITE FOR RESIDUE EDO A2496
06AC6SOFTWAREASP A:1204 , GLN A:1489 , HOH A:2163 , HOH A:2164 , PRO B:1183 , SER B:1184 , PHE B:1201BINDING SITE FOR RESIDUE EDO A2497
07AC7SOFTWAREASP A:1330 , MET A:1370 , HOH A:2015BINDING SITE FOR RESIDUE EDO A2498
08AC8SOFTWAREARG A:1191 , LYS B:1190 , ARG B:1191 , TYR B:1497BINDING SITE FOR RESIDUE EDO B2501
09AC9SOFTWARESER A:1227 , THR A:1228 , GLY A:1401 , ASN A:1476BINDING SITE FOR RESIDUE EDO A2499
10BC1SOFTWARETYR A:1376 , LYS A:1378 , THR A:1384 , HIS A:1387 , GLU A:1389 , ASN A:1397 , TRP A:1407 , ILE A:1461 , HIS A:1467 , ASN A:1477 , HOH A:2103 , NI A:2494BINDING SITE FOR RESIDUE 8XQ A3001
11BC2SOFTWARETYR B:1376 , LYS B:1378 , THR B:1384 , HIS B:1387 , GLU B:1389 , ASN B:1397 , TRP B:1407 , HIS B:1467 , HOH B:2091 , HOH B:2155 , NI B:2500BINDING SITE FOR RESIDUE 8XQ B3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XXZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:1401 -Pro A:1402
2Gly B:1401 -Pro B:1402

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XXZ)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM6B_HUMAN1339-1502
 
  2A:1336-1493
B:1336-1499
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM6B_HUMAN1339-1502
 
  1A:1336-1493
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.KDM6B_HUMAN1339-1502
 
  1-
B:1336-1499

(-) Exons   (0, 0)

(no "Exon" information available for 2XXZ)

(-) 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:292
 aligned with KDM6B_HUMAN | O15054 from UniProtKB/Swiss-Prot  Length:1643

    Alignment length:319
                                  1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487         
         KDM6B_HUMAN   1178 REKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLA 1496
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..hhhhh.hhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhh.....---------------------------..eeeeeeeee..hhhhhhhhhhhhh..hhhhh........ee..ee......eeeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeeee...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:1336-1493 UniProt: 1339-1502                                                                                                                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xxz A 1175 REKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEE---------------------------HHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLA 1493
                                  1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284       | -         -         -     |1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484         
                                                                                                                                              1292                        1320                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with KDM6B_HUMAN | O15054 from UniProtKB/Swiss-Prot  Length:1643

    Alignment length:325
                                  1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497     
         KDM6B_HUMAN   1178 REKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEKESEDEESEEPDSTTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEW 1502
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-2xxzB01 B:1374-1482                                                                                     ----------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-2xxzB02 B:1374-1482                                                                                     ----------------- Pfam domains (2)
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhh-----------------------------..eeeeeeeee......hhhhhhhhh..hhhhh....----------.......eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: B:1336-1499 UniProt: 1339-1502                                                                                                                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xxz B 1175 REKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQ-----------------------------HHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTST----------ILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEW 1499
                                  1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284     |   -         -         -     |1324      1334      1344      1354 |       -  |   1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484      1494     
                                                                                                                                            1290                          1320                                1356       1367                                                                                                                                    

   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 2XXZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XXZ)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Family: JmjC (39)
1aJmjC-2xxzB01B:1374-1482
1bJmjC-2xxzB02B:1374-1482

(-) 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 4ask 5fp3

(-) Related Entries Specified in the PDB File

2xue CRYSTAL STRUCTURE OF JMJD3