triangle PDBeMotif: 3avs  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
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Enzyme   1.14.11.
Classification oxidoreductase    | release date: Mon, Mar 7, 2011
Title catalytic fragment of utx/kdm6a bound with n-oxyalylglycine, ni(ii)
Authors S.YOKOYAMA, T.SENGOKU
Method X-RAY DIFFRACTION (resolution: 1.85Å)
PDBe Citation   
Small molecules:    search ZN ZN binding statistics ZN   search NI NI binding statistics NI   search OGA OGA binding statistics OGA   search CL CL binding statistics CL   search EDO EDO binding statistics EDO
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
GPGYQDPNSQIIPSMSVSIYPSSAEVLKACRNLGKNGLSNSSILLDKCPPPRPPSSPYPPLPKDKLNPPTPSIYLENKRD
AFFPPLHQFCTNPNNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWHCESNRSHT
TIAKYAQYQASSFQESLREENEKRSHHKDHSDSESTSSDNSGRRRKGPFKTIKFGTNIDLSDDKKWKLQLHELTKLPAFV
RVVSAGNLLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEGYWGVLNDFCEKNNLNFLM
GSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAIGWCNNIAWNVGPLTACQYKLAVERYEWNKLQSVKSIVPM
VHLSWNMARNIKVSDPKLFEMIKYCLLRTLKQCQTLREALIAAGKEIIWHGRTKEEPAHYCSICEVEVFDLLFVTNESNS
RKTYIVHCQDCARKTSGNLENFVVLEQYKMEDLMQVYDQFTLAPPLPSASS
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain A : LYSINE-SPECIFIC DEMETHYLASE 6A
member of: PANTHER:searchPTHR14017/searchPTHR14017_SF9PFAM:searchPF02373PROSITE PROFILES:searchPS51184, SMART:searchSM00558SUPERFAMILY:searchSSF51197UniProt:searchO15550
JMol viewer RasMol script viewer  EDO 1516A  ..                 ..                                                                                                                                           ..EDO ..                              *  *  **                                                                                                                                                                                                                                                                                        
JMol viewer RasMol script viewer  EDO 1515A  ..                 ..                              *                              *                                                                             ..EDO ..                              |  |  ||                                                                                                                                                                                                                                                                                        
JMol viewer RasMol script viewer  EDO 1514A  ..                 ..                              |                              |             **                                                    *         ..EDO ..                              |  |  ||                                            **                                                                        **                                                                                                                                                                
JMol viewer RasMol script viewer  EDO 1513A  ..                 ..                              |                              |         **  *|                                                    |         ..EDO ..                              |  |  ||                                           *||                                                                        ||                                                                                                                                                                
JMol viewer RasMol script viewer  EDO 1512A  ..                 ..                              |                              |         ||  ||                                                    |         ..EDO ..                              |  |  ||                                           |||                                                                        ||              *  *                                                                                                                                              
JMol viewer RasMol script viewer  EDO 1511A  ..                 ..                              |                              |         ||  ||                                                    |         ..EDO ..                              |  |  ||                                           |||                                                   **                   ||              |  |                                                                                                                                              
JMol viewer RasMol script viewer  EDO 1510A  ..                 ..                              |                              |         ||  ||                                           *   **   |         ..EDO ..     *                        |  |  ||                                           |||                                                   ||                   ||              |  |                                                                                                                                              
JMol viewer RasMol script viewer  EDO 1509A  ..                 ..                  *           |                              |         ||  ||                                           |   ||   |         ..EDO ..     |                        |  |  ||                                           |||                                                   ||                   ||              |  |                                                                                                                                              
JMol viewer RasMol script viewer  EDO 1508A  ..                 ..                  |           |                              |         ||  ||                                           |   ||   |         ..EDO ..     |                        |  |  ||                                           |||                                                   ||                   ||              |  *  **                                     *  *                                                                                                 
JMol viewer RasMol script viewer  EDO 1507A  ..                 ..                  |           |                              |         ||  ||                                           |   ||   |         ..EDO ..     |                        |  |  |*     *                                     |||                                                   ||                   ||              |  |  ||                                     |  |                                                                                                 
JMol viewer RasMol script viewer  CL 1506A  ..                 ..                  |           |                              |         ||  ||                                        *  |   ||   |         ..CL ..     |                        |  |  ||     |                                     |||                                                   ||                   ||              |  |  ||                                     |  |                                                                                                 
JMol viewer RasMol script viewer  NI 1505A  ..                 ..                  |           |                              |         ||  ||                                        |  |   ||   |         ..NI ..     |                        |  |  ||     |                                     |||                                                   ||                   ||              |  |  ||                                     |  |                                                                                                 
JMol viewer RasMol script viewer  NI 1504A  ..                 ..                  |           |                              |         ||  ||                                        |  |   ||   |         ..NI ..     |                        |  |  ||     |                                     |||                                                   ||                   ||              |  |  ||                                     |  |                                                                                                 
JMol viewer RasMol script viewer  NI 1503A  ..                 ..                  |           |                              |         ||  ||                                        |  |   ||   |         ..NI ..     |                        |  |  ||     |                        * *          |||                                                   ||           *       ||              |  |  ||                                     |  |                                                                                                 
JMol viewer RasMol script viewer  ZN 1502A  ..                 ..                  |           |                              |         ||  ||                                        |  |   ||   |         ..ZN ..     |                        |  |  ||     |                        | |          |||                                                   ||           |       ||              |  |  ||                                     |  |                                *  *                       *  *                                  
JMol viewer RasMol script viewer  OGA 1501A  ..                 ..                  |           |                              |         ||  ||                                        |  |   ||   |         ..OGA ..     |                        |  |  ||     |               *     *  * *     * *  |||    *                                              ||           * *     ||  *           |  |  ||                                     |  |                                |  |                       |  |                                  
sec str:  ........hhhhhhhhhh.........................hhhhh.....eee..hhhhhh.hhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhh.... .....eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhhh.....
sequence :  ..SVSIYPSSAEVLKACRN..NSSILLDKCPPPRPPSSPYPPLPKDKLNPPTPSIYLENKRDAFFPPLHQFCTNPNNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWHCESNRSHTTIAKYAQYQASSFQESLR... ..PFKTIKFGTNIDLSDDKKWKLQLHELTKLPAFVRVVSAGNLLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEGYWGVLNDFCEKNNLNFLMGSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAIGWCNNIAWNVGPLTACQYKLAVERYEWNKLQSVKSIVPMVHLSWNMARNIKVSDPKLFEMIKYCLLRTLKQCQTLREALIAAGKEIIWHGRTKEEPAHYCSICEVEVFDLLFVTNESNSRKTYIVHCQDCARKTSGNLENFVVLEQYKMEDLMQVYDQFTLAPP
seq num:  ..886       896    ..910       920       930       940       950       960       970       980       990       1000      1010      1020      1030      1040     ... ..1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388    
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..      |  || |||| ..^*** | |               |  |             |  |     |  |  |      | || |||  |  ||||| |||  |          || |  | |||||| |  |^***      |  |  || || |..PS00001..   | | || ||| |     || |||  | |  |  | ||   || | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  ||||| ||  |||| ||  | | ||| ||| || |||||||  | |||| || |      ||  |   | | ||| |  |    ^***||||||       | ||||||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..      |  || |||| ..  |  | |               |  |             |  |     |  |  |      | || |||  |  ||||| |||  |          || |  | |||||| |  | |        |  |  || || |..PS00004..   | | || ||| |     || |||  | |  |  | ||   || | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  ||||| ||  |||| ||  | | ||| ||| || |||||||  | |||| || |      ||  |   | | ||| |  |    |  |||||||       **^*||||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..      |  || |||| ..  |  | |               |  |             |  |     |  |  |      | || |||  |  ^**|| |||  |          || |  | ||^**| |  ^**        |  |  || |^**..PS00005..   ^** || ||| |     || |||  | |  |  | ||   || | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  |^**| ||  |||| ||  | | ||| ||| || |||^**|  ^**||| || |      ||  |   | | ||| |  |    |  |^**|||       |  |||||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..      ^***| |||| ..  |  | |               |  |             |  |     |  |  |      | || |||  |  |||^***||  |          || |  | |||| | |             |  |  ^***^**..PS00006..       |^***| |     || |||  | |  |  | ||   || | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  | | | ||  |||| ||  | | ||| ||| || |||||||  ^***|| || |      |^***   | ^***| |  |    |  | |||||       |  |||||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..         || |||| ..  |  | |               |  |             |  |     |  |  |      | || |||  |  ||| |  ||  |          || |  | |||| | |             |  |  ||     ..PS00007..       |  | | |     || |||  | |  |  | ||   || | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  | | | ||  |||| ||  | | ||*******^ |||||||      || || |      ********^   | | |  |    |  | |||||       |  |||||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..         || |||| ..***  | |               |  |             |  |     |  |  |      ^*****||  ^***** |  ||  |          || |  | |||| | |             |  |  ||     ..PS00008..       |  | | |     || |||  | |  |  | ^*****| | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  | | | ||  |||| ||  | | ||| ||| || |||||||      || || |       |  |       | | |  |    |  | |||||       |  |^*****        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  AMIDATION ..         || |||| ..     | |               |  |             |  |     |  |  |      | || |||  |  ||  |  ||  |          || |  | |||| | |             |  |  ||     ..PS00009..       |  | | |     || |||  | |  |  |  |    | | | |||       |  |                  | |            |  || || | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  | | | ||  |||| ||  | | ||| ||| || |||||||      || || |       |  |       | | |  |    |  | |||||       |  | |||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..         |*****| ..     | |               |  |             |  |     |  |  |      | || |||  |  ||  |  ||  |          || |  | |||| | |             |  *****     ..alphabetamotif..       |  | | |     || |||  | |  |  |  |    | | | |||       |  |                  | |            ******** | | |  |    | |    | |       |  |    |  |                    |   **********|  | | | |*****|| ||  | | ||***** *********|      ***** |       |  |       | | |  |    |  | |||||       |  | |||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  asxmotif ..         || || | ..     | |               |  |             |  |     |  |  |      | || |||  |  ||  |  ||  |          || |  | |||| | |             |  |  |      ..asxmotif..       |  | | |     || |||  | |  |  |  |    | | | |||       |  |                  | |            |  |  |  | | |  |    | |    | |       |  |    |  |                    |   ||||||| |||  | | | ||  | || ||  | | *****|| || || || |      || || |       |  |       | | |  |    |  | |||||       |  | |||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  asxturn ..         || || | ..     | |               |  |             |  |     |  |  |      | || |||  |  ||  |  ||  |          || |  | |||| | |             |  |  |      ..asxturn..       |  | | |     || |||  | |  |  |  |    | | | |||       |  |                  | |            |  |  |  | | |  |    ***    | |       |  |    |  |                    |   ||||||| |||  | | | ||  | || ||  | | ||| ||| || || || |      || || |       |  |       | | |  |    |  | |||||       |  | |||||        |  |  |  |     
search RasMol script viewer Motif-ligand binding stats  betaturn ..         ******* ..     | |               ****             |  |     |  |  |      | |****|  |  |*******|  |          ****  ****|| | |             *******      ..betaturn..       |  | | |     *****|  | ****  |  |    | | ****|       ****                  | |            *******  | | |  |           | |       |  |    |  |                    |   ************** | | |**** *****  | | |*****************      ***** |       |  |       | | |  |    **** |||||       |  ****|||        **********     
search RasMol script viewer Motif-ligand binding stats  nest ..                 ..     | |                                |  |     |  |  |      ***  ***  |  |       |  |           | |    **** | |                          ..nest..       |  | | |          |  | |  |  |  |    ***   ***       |  |                  | |                     *** |  |           ***       |  |    |  |                    |   |            *** | |         |  | | |                           ***       |  |       *** |  |         *****       |  | ****|              |  |     
search RasMol script viewer Motif-ligand binding stats  niche ..                 ..     ***                                ****     *******        |    |  ****       ****           ***         ***                          ..niche..       **** ***          **** ****  ****                    ****                  ***                         ****                     ****    ****                    |   |                ***         **** ***                                     ****           ****                     ****  ****              ****     
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..                 ..                                                                ******                                                                     ..schellmannloop..                                                                                                                                                                       |   |                                                                                                                                                  
search RasMol script viewer Motif-ligand binding stats  stmotif ..                 ..                                                                                                                                           ..stmotif..                                                                                                                                                                       *****                                                                                                                                                  

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