Bacterial Sialidase

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

  Property   Value
  Name Bacterial Sialidase
  Conformer 1
(PDB)
1eut (A)
  Conformer 2
(PDB)
2ber (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 118 0.96   402 - 404   407 - 428   431 - 491   495 - 505   552 - 553   556 - 558   565 - 565   567 - 571   611 - 613   622 - 625   641 - 641   643 - 644
2 358 0.6   51 - 401   405 - 406   429 - 430   492 - 494
3 119 0.82   506 - 551   554 - 555   559 - 564   566 - 566   572 - 610   614 - 621   626 - 640   642 - 642   645 - 645

Sequence


           ________________________________________________________________________________________________________________________ 
 1eut(A) : GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIDAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPAD 
         :                                                                                                                          
 2ber(A) : GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIDAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPAD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1eut(A) : PNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDENKTVELSDGRVLLNSRDSARSGYRKV 
         :                                                                                                                          
 2ber(A) : PNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDENKTVELSDGRVLLNSRDSARSGYRKV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________401_____ 
 1eut(A) : AVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICA 
         :                                                                                                                          
 2ber(A) : AVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSGSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICA 
           ________________________________________________________________________________________________________________401_____ 

           ___________________428____________________________________________________________491___________505_____________________ 
 1eut(A) : PFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRA 
         :                                                                                                                          
 2ber(A) : PFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRA 
           ___________________428____________________________________________________________491___________505_____________________ 

           ______________________551____558___564____571____________________________________610________621_625____________640______ 
 1eut(A) : SNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQ 
         :                                                                                                                          
 2ber(A) : SNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQ 
           ______________________551____558___564____571____________________________________610________621_625____________640______ 

           _                                                                                                                        
 1eut(A) : R                                                                                                                        
         :                                                                                                                          
 2ber(A) : R                                                                                                                        
           _                                                                                                                        

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
7.4
Translation
(A)
1.1
Closure
(%)
71.6
Bending Residues
( green )
  401 - 402
  404 - 407
  428 - 434
  491 - 492
  494 - 495
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
7.9
Translation
(A)
0.2
Closure
(%)
91.5
Bending Residues
( green )
  505 - 506
  551 - 556
  558 - 559
  564 - 568
  571 - 572
  610 - 611
  613 - 614
  621 - 622
  625 - 626
  640 - 645
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Shear

PyMOL Script

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