triangle PDBeMotif: 2v3d  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
AstexViewer TM
Download original PDB file
Download xml file
Download structure factors file
Enzyme   3.2.1.45
Classification hydrolase    | release date: Sun, Jun 17, 2007
Title acid-beta-glucosidase with n-butyl-deoxynojirimycin
Authors A.H.FUTERMAN, B.BRUMSHTEIN, D.AVIEZER, H.M.GREENBLATT, I.SILMAN, J.L.SUSSMAN, T.D.BUTTERS, Y.SHAALTIEL
Method X-RAY DIFFRACTION (resolution: 1.96Å)
PDBe Citation   
Small molecules:    search BMA BMA binding statistics BMA   search NAG NAG binding statistics NAG   search FUC FUC binding statistics FUC   search NBV NBV binding statistics NBV   search SO4 SO4 binding statistics SO4
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chains A,B sequence:
EFARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKV
KGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKI
PLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSA
GLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLA
PAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFV
DSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVG
FLETISPGYSIHTYLWHRQLLVDTM
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 : GLUCOSYLCERAMIDASE
member of: CATH:search2.60.40.1180/search3.20.20.80GENE3D:searchG3DSA_2.60.40.1180/searchG3DSA_3.20.20.80PANTHER:searchPTHR11069/searchPTHR11069_SF9PFAM:searchPF02055PRINTS:searchGLHYDRLASE30SUPERFAMILY:searchSSF51011/searchSSF51445UniProt:searchP04062
JMol viewer RasMol script viewer  SO4 1506A  ..                             ..                                                                                                                                                                 **                                               **                                                                                                                                                                                                                                                               
JMol viewer RasMol script viewer  SO4 1505A  ..                             ..                                                                                                                                                                 ||                                               ||                                         *                                                                               *                                                                                                                                     
JMol viewer RasMol script viewer  SO4 1504A  ..                             ..                                               *                                                                                                                 ||                                 *             ||                                 *       |                    *                                                          |                                                                                                                                     
JMol viewer RasMol script viewer  NBV 1503A  ..                             ..                                               |                                               **                                                  *             ||                                 |     **      ||  *                              |       |                    |      *                          *    *                   |               *              *                                                                                                      
JMol viewer RasMol script viewer  SO4 1502A  ..            **               ..                                               |                                               ||                                                  |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |       *  * *      |               |              |                                                                                                      
JMol viewer RasMol script viewer  NAG 1498A  ..            ||      *  *     ..                                               |                                               ||                                                  |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |       |  | |      |               |              |                                                                                                      
JMol viewer RasMol script viewer  NAG 1499A  ..            ||      |  *     ..                                               |                                               ||                                                  |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |       |  | |      |               |              |                                                                                                      
sec str:  .........ee.......eeee...............eeeeeeee......eeeeee.........eeeeeeeeeeeee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhh.......eeeeee..........................hhhhhhhhhhhhhhhhhhh....eeeeee...hhhh.................hhhhhhhhhhhhhhhhhhhhh.....eee...hhhhhhh..........hhhhhhhhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhh...eeeee..hhhhh....hhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhhhh.eeeeeeee...................eeeehhhheeeehhhhhhhhhhhh......eeeeeee.....eeeeeee.....eeeeeee.....eeeeeee...eeeeeee...eeeeeee....
sequence :  ..EFARPCIPKSFGYSSVVCVCNATYCDSFD..PALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQL
seq num:  ..-1        9         19       ..32        42        52        62        72        82        92        102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492    
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..         ||||       ^*** |   ..      |  ||||||||          ^*** |    ||  |        |    |     |  |          |  |  || | |          | |  | |||  | |||^*** |             |  | |            |  | |||   ||| | |  |                || |||         | |||||  |       |   |      |   || ^***  |        |  |    | | || | |  |             |   |  || | |  |     | | | |  | | |  |   |    |    |  | |          | ||| | |||           | |   |  |          |  | | |   |||| |      | |||      ^***||   | ||                        
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..         ||||       | || |   ..      |  |^**^**|             | |    ||  |        |    |     |  |          |  |  || | |          ^**  | |||  | ||||||  |             |  | |            |  | |||   ||^** |  |                || |||         | |||||  |       |   |      |   ||  | |  |        |  |    | | || | |  |             |   |  |^** |  |     | | | |  | ^**  |   |    |    |  | |          | ||| | |||           | |   |  |          |  ^** |   ^**| |      | |||      | ^**|   ^**|                        
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..         ||||       | ^***   ..      ^*** | ||||             | |    ||  |        |    |     |  |          |  |  || | |               ^***^*** |||||^***             |  | |            |  | |||   ||    |  |                || |||         | |||||  |       |   |      |   ||  | |  |        |  |    | | ^*** |  |             |   ^***|   |  |     | | | |  |   |  |   |    |    |  | |          | ||| | |||           | |   |  |          |  |   |    | | |      | |||      | ^***   ^***                        
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..         ||||       |  |     ..           | ||||             | ^*****|  |        ^*****     |  |          |  |  ^*****               | | |  | |||||                 |  | |            |  | |^*****^*****  |                || |||         | ||^*****       |   |      |   ||  | |  |        |  |    | | || | |  |             |   |   |   |  |     | | | |  |   |  |   ^*****    |  | |          | ||| | |||           | |   |  |          |  |   ^***** | |      | |||      | | |                                
search RasMol script viewer Motif-ligand binding stats  AMIDATION ..         ||||       |  |     ..           | ^***             | |     |  |                   |  |          |  |  || |                 | | |  | |||||                 |  | |            |  | | |         |  |                || |||         | || ||  |       |   |      |   ||  | |  |        |  |    | | || | |  |             |   |   |   |  |     | | | |  |   |  |             |  | |          | ||| | |||           | |   |  |          |  |          | |      | |||      | | |                                
search RasMol script viewer Motif-ligand binding stats  asxmotif ..         ||||       |  |     ..           | |||              | |     |  |                   |  |          |  |  || |                 | | |  | |||||                 |  | |            |  | | |         |  |                || |||         | || ||  |       |   |      |   ||  | |  |        |  |    | | || | |  |             |   |   |   |  |     | | | |  |   |  |             |  | |          | ||| *****           | |   |  |          |  |          | |      | |||      | | |                                
search RasMol script viewer Motif-ligand binding stats  asxturn ..         ||||       |  |     ..           | |||              | |     |  |                   |  |          |  |  || |                 | | |  | |||||                 |  | |            |  | | |         |  |                || |||         | || ||  |       |   |      |   ||  | |  |        |  |    | | |*** |  |             |   |   |   |  |     | | | |  |   |  |             |  | |          | ||| ***||           | |   |  |          |  |          ***      | ***      *** |                                
search RasMol script viewer Motif-ligand binding stats  betabulgeloop ..         ||||       |  |     ..           *****              | |     |  |                   |  |          |  |  || |                 | | |  | |||||                 |  | |            |  | | |         |  |                || |||         | || ||  |       |   |      |   ||  | |  |        |  |    | | ||   |  |             |   |   |   |  |     | | | |  |   |  |             |  | |          ***** | |||           | |   |  |          |  |          | |      | |||      | | |                                
search RasMol script viewer Motif-ligand binding stats  betaturn ..         ||||       |  |     ..           ****|              | |     |  |                   |  |          |  ****| |                 | | |  ****|||                 |  | |            |  | | |         ****                *****|         **********       |   |      |   ||  | ****        ****    | | ||   |  |             |   |   |   |  |     | | | ****   ****             **** |          ****| ****|           | |   ****          ****          | |      ****|      | | |                                
search RasMol script viewer Motif-ligand binding stats  nest ..         |***       |  |     ..             ***              | |     |  |                   |  |          |  |   ***                 | | |    ****|                 |  | |            |  | ***                             |  ***         |  |  |  |       |   |      |   ||  | |  |        |  |    | | ||   |  |             |   |   |   |  |     | | ***  |   |  |                ***            ***   ***           ***                 |  |          | |        ***      | | |                                
search RasMol script viewer Motif-ligand binding stats  niche ..         | |        ****     ..                              ***     ****                   ****          ****                       | ***     ****                 ******            ****                                 |    |         |  *******       |   |      |   |**** ****        ****    | ****   ****             |   |   |   ****     | | ******   ****                                                                       ****          ***                 *****                                
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..         | |                 ..                                                                                                      | |                                                                                   ******         |                |   |      |   |   | |                   |   |                     |   |   |            | |                                                                                                                         | |                                
search RasMol script viewer Motif-ligand binding stats  stmotif ..         | |                 ..                                                                                                      | |                                                                                                  |                *****      |   |   | |                   |   |                     |   |   |            | |                                                                                                                         | |                                
search RasMol script viewer Motif-ligand binding stats  ststaple ..         | |                 ..                                                                                                      | |                                                                                                  |                           *****   | |                   *****                     *********            | |                                                                                                                         | |                                
search RasMol script viewer Motif-ligand binding stats  stturn ..         ***                 ..                                                                                                      ***                                                                                                  |                                   ***                                                                  | |                                                                                                                         ***                                
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..                             ..                                                                                                                                                                                                           *                                                                                                        * *                                                                                                                                                            

Assembly 2     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 B : GLUCOSYLCERAMIDASE
member of: CATH:search2.60.40.1180/search3.20.20.80GENE3D:searchG3DSA_2.60.40.1180/searchG3DSA_3.20.20.80PANTHER:searchPTHR11069/searchPTHR11069_SF9PFAM:searchPF02055PRINTS:searchGLHYDRLASE30SUPERFAMILY:searchSSF51011/searchSSF51445UniProt:searchP04062
JMol viewer RasMol script viewer  SO4 1507B  ..                                                                                                                                                                                                **                                               **                                                                                                                                                                                                                                                              
JMol viewer RasMol script viewer  SO4 1506B  ..                                                                                                                                                                                                ||                                               ||                                         *                                                                               *   *                                                                                                                                
JMol viewer RasMol script viewer  SO4 1505B  ..                                                                              *                                                                                                                 ||                                 *             ||                                 *       |                    *                                                          |   |                                                                                                                                
JMol viewer RasMol script viewer  NBV 1504B  ..                                                                              |                                               **                                                  *             ||                                 |     **      ||  *                              |       |                    |      *                          *    *                   |   |           *              *                                                                                                     
JMol viewer RasMol script viewer  NAG 1503B  ..                                                                              |                                               ||                **                                |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |                   |   |           |              |                                                                                                     
JMol viewer RasMol script viewer  SO4 1502B  ..          **                                                                  |                                               ||                ||                                |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |       *  * *      |   |           |              |                                                                                                     
JMol viewer RasMol script viewer  NAG 1498B  ..          ||      *  *                                                        |                                               ||                ||                                |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |       |  | |      |   |           |              |                                                                                                     
JMol viewer RasMol script viewer  NAG 1499B  ..          ||      |  *                                                        |                                               ||                ||                                |             ||                                 |     ||      ||  |                              |       |                    |      |                          |    |       |  | |      |   |           |              |                                                                                                     
sec str:  .......ee.......eeee.................eeeeeeee......eeeeee.........eeeeeeeeeeeee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhh.......eeeeee..........................hhhhhhhhhhhhhhhhhhh....eeeeee...hhhh.................hhhhhhhhhhhhhhhhhhhhh.....eee...hhhhhhh..........hhhhhhhhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhhhh.eeeeeeee...................eeeehhhheeeehhhhhhhhhhhh......eeeeeee.....eeeeeee.....eeeeeee.....eeeeeee...eeeeeee...eeeeeee...
sequence :  ..ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491    
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..       ||||       ^*** |             |  ||||||||          ^*** |    ||  |        |    |     |  |          |  | ||| | |          | |  | |||  | |||^*** |             |  | |            |  | |||   ||| | |  |   |            || |||         | |||||  |       |   |      |   || ^***  |        |  |      | || ||| ||         |  |    |  || | |  |     | | | |  | | |  |   |    |    |  | |          | ||| | |||           | |                 |  | | |   |||| |      | |||      ^***||   | ||                       
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..       ||||       | || |             |  |^**^**|             | |    ||  |        |    |     |  |          |  | ||| | |          ^**  | |||  | ||||||  |             |  | |            |  | |||   ||^** |  |   |            || |||         | |||||  |       |   |      |   ||  | |  |        |  |      | || ||| ||         |  |    |  |^** |  |     | | | |  | ^**  |   |    |    |  | |          | ||| | |||           | |                 |  ^** |   ^**| |      | |||      | ^**|   ^**|                       
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