Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  FREE KDM6B STRUCTURE
 
Authors :  Z. J. Cheng, D. J. Patel
Date :  02 May 12  (Deposition) - 08 Aug 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mjd3/Kdm6B, Jmjc Domain, Histone 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: 1.14.112
    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 , HIS A:1390 , GLU A:1392 , SER A:1398 , ASN A:1400 , ILE A:1464 , HIS A:1470 , ALA A:1482 , NI A:1702BINDING SITE FOR RESIDUE OGA A 1701
2AC2SOFTWAREHIS A:1390 , GLU A:1392 , HIS A:1470 , OGA A:1701BINDING SITE FOR RESIDUE NI A 1702
3AC3SOFTWARECYS A:1575 , CYS A:1578 , CYS A:1602 , CYS A:1605BINDING SITE FOR RESIDUE ZN A 1703
4AC4SOFTWARELYS B:1381 , THR B:1387 , HIS B:1390 , GLU B:1392 , SER B:1398 , ASN B:1400 , HIS B:1470 , VAL B:1472 , ALA B:1482 , NI B:1702BINDING SITE FOR RESIDUE OGA B 1701
5AC5SOFTWAREHIS B:1390 , GLU B:1392 , HIS B:1470 , OGA B:1701BINDING SITE FOR RESIDUE NI B 1702
6AC6SOFTWARECYS B:1575 , CYS B:1578 , CYS B:1602 , CYS B:1605BINDING SITE FOR RESIDUE ZN B 1703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EZ4)

(-) 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 4EZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EZ4)

(-) 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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh...........hhhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhh..hhhhhhhhhhhhhh...eeeeeee......................eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeee......hhhhhh.....hhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhh..........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.........ee......ee...eeee....eeehhhhhhhhh......eeee..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ez4 A 1157 ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEEIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSETYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475      1485      1495      1505      1515      1525      1535      1545      1555      1565      1575      1585     |1600      1610      1620      1630        
                                                                                                                                                                   1295|                                                                                                                                                                                                                                                                      1591|                                         
                                                                                                                                                                    1325                                                                                                                                                                                                                                                                       1597                                         


Chain B from PDB  Type:PROTEIN  Length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh........hhhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhh.......hhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhh..eeeeeeeee......hhhhhhhh...hhhhh.....hhhhh...........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhh..........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.........ee......ee...eeee....eeehhhhhhhhh......eeee..hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ez4 B 1157 ESYLSPAQSVKPKIEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSETYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAPA 1639
                                  1166   || 1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289    ||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       
                                      1170|                                                                                                                    1294|                                                                                                                                                                                                                                                                        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 4EZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EZ4)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:1404 - Pro A:1405   [ RasMol ]  
    Gly B:1404 - Pro B:1405   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ez4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KDM6B_MOUSE | Q5NCY0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.112
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KDM6B_MOUSE | Q5NCY0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4ask KDM6B BOUND WITH A SPECIFIC INHIBITOR
4eyu FREE MOUSE KDM6B IN P212121 SPACE GROUP.
4ezh